If you're running Win7, you'll need drivers for USB 3.0.  Any OS after that is no longer needed.  W7 64bit > http://cdn.evga.com/Driver/X99/8-29-2014_(Launch_release)/USB3.0.zip
 
As far as BIOS settings, there are USB settings there, but since it sounds like it works to some degree, I'd assume they are all on/enabled.  They are enabled by default as well.

I don't have any USB 3.0 devices to test with.  I've always had my mouse & keyboard plugged into USB 2.0 ports.  I did just plug my mouse into a USB 3.0 port and heard the driver load.  I rebooted to see if I would encounter anything unusual.  All was good there.  So far for the little I've used my mouse (3.0 port), all is good so far.  I'll continue using my mouse connected to the 3.0 port to see if I notice anything unusual.

My USB 3.0 is worthless for me, even if I use a USB 2.0 drive in it. Both 3.0 and 2.0 drives will lock up on longer transfers and using the 3.0 ports will cause my mouse and keyboard in the 2.0 ports to mess up.

I'm in the process of copying about 8GB worth of documents to a USB 2.0 flash drive connected to a USB 3.0 port to see how it works.  2GB in so far with no issue's.

The only other thing I could suggest is to enter the BIOS > Advanced tab > USB Config > Verify that "Legacy USB support" is enabled, "XHCI Mode" is set to Smart Auto, and all USB ports & headers are enabled.
 
BTW, all 8GB transferred to a USB 2.0 drive connected to a USB 3.0 port without issue.

GTXJackBauer
Make sure your back I/O MB cover isn't bugging things out.  Try without the cover and see if the problem persists.  
 
Could also be a bad USB 3.0 cable/header.

It's both the rear ports and the cable/header port. I've had this board in 2 different cases since I have had it and it's always done this. Always figured a bios update or driver would fix it. Getting close to the end of my warranty and if I have a faulty board I need to get it taken care of before the warranty runs out.
 
So you have no issue with USB 3.0 on your X99 Classy?

I can shine some light on this issue as I've been dealing with this for over  year, this USB 3.0/3.1 issue is knowing to be a big problem across  all boards manufactures, specifically on x99 platform.
 
It will randomly sneak upon you when you leas expected and either lack up your  whole PC, or hang your windows while entering sleep mode and other things. I was troubleshooting this issue for about 12-15 months because it's so intermittent, it will be all fine for day or
 
even week and just when you think its fixed, bang...again I didn't realize that USB 3 would cause this much of a problems.
 
It's not as bad on Win 10 but still happens, on windows 7 the eXtensible host controller and drivers are awful, they give your  good speed but at what cost, its not worth it. I had 3 M/B replacement and 2 different M/B brands all x99 the same problems.
 
My final fixed was to not installing USB drivers and even thou my Das keyboard uses USB3 I can live without it to avoid the issues I was having, it's all good now and even when I'm using USB devices the speed is of USB 2 that's OK, it takes bit longer but I'm much
 
happier now.
 
reconsider your RMA, your M/B might be just fine
 

I'm on windows 7 x64 Pro and I couldn't bare with that problem, it took me literally over a year to figure that out so I just didn't bother installing the host controller and drivers, no big deal from me.
 
The only problem I have is that Daz keyboard like to be connected directly to USB3 port, otherwise its not detected outside windows, again no big deal I use old simple keyboard if I need to use it in that case.
 
Windows 10 have drivers built in to OS, yet you can still get the new host controller from Intel. What I'm saying is that the x99 platform ALL across brands different have issues with USB 3 not so much on windows 10 but you still will have sporadic issues come and go and because of the intermittent nature of it, its unpredictable when will accrue again.
 
For example, in some cases people don't even know they have that issue if say...they don't use sleep mode and just let their PC run all the time and shot down  before bad time, otherwise random hanging entering sleep mode. Another issue is black screen on boot, or freezes windows logo, or PC hangs, all that is so darn random that no one knows when will happen and its all because of the USB 3 host controller and drivers.
 
Put is this way, I got to the same answers from 2 different M/B makers, Asus and Gigabit and they told me straight out "We will not update any drivers for compatibility with USB 3 and x99 platform at this point" windows 7 is to old and windows 10 have their own drivers, so they moving forward to new x299 platform.
 
Ever since I left the USB 3 drivers behind my system never been this stable. Don't get me wrong, when I had the Host controller and drivers installed things were working very smooth, all USB 3 ports great transfer speed was 3 times faster what I have now, but every time I would put my system to sleep I was worry is it going to happen again and I could go for days and in between  I was troubleshooting with Asus and just when I thought I got it and I was blaming my network forensic software...happen again and this was for a damn very long time troubleshooting.
 
I installed windows 10 to see if maybe the OS is messing things up, It was fine fro almost 2 weeks so at least I knew it wasn't my hardware and just before I switched back to Win 7.. bang on and happen again.
 
So! if you on x99 and windows 10 and if you don't want to have any kind of strange issues I would just leave Intel USB 3.0 extensible host controller alone, its more trouble than help

Yap,  x99 is very good M/B  and works flawlessly if I don't install USB 3 drivers, which tbh. I don't really  need
 
 

kram36

GTXJackBauer
Make sure your back I/O MB cover isn't bugging things out.  Try without the cover and see if the problem persists.  
 
Could also be a bad USB 3.0 cable/header.

It's both the rear ports and the cable/header port. I've had this board in 2 different cases since I have had it and it's always done this. Always figured a bios update or driver would fix it. Getting close to the end of my warranty and if I have a faulty board I need to get it taken care of before the warranty runs out.
 
So you have no issue with USB 3.0 on your X99 Classy?

I've had issues in the past with both USB 2.0 and 3.0 from the rear I/O panel.  Mainly with the Sennheiser PC363D.  I would get crazy static through my mic.  Checked everything, drivers, etc. and couldn't figure out the issue.  I moved to the front USB 3.0 (cases's 3.0 cable to MB's internal 3.0 header) and the issue went away like it never happened. 
 
The X99 Classy can be finicky at times.

GTXJackBauer
I've had issues in the past with both USB 2.0 and 3.0 from the rear I/O panel.  Mainly with the Sennheiser PC363D.  I would get crazy static through my mic.  Checked everything, drivers, etc. and couldn't figure out the issue.  I moved to the front USB 3.0 (cases's 3.0 cable to MB's internal 3.0 header) and the issue went away like it never happened. 
 
The X99 Classy can be finicky at times.

It's both the rear i/o and the front panel USB 3.0 ports for me.

bdary
Still no issue's here with my mouse connected to a USB 3.0 port.  Booting, in & out of sleep often, gaming, and general use (6 - 8 hrs a day) without issue.

Are U on Win 10 or 7, sorry maybe you have mentioned somewhere earlier.
Do you put your system to sleep/hibernation, if you don't, try it for few days, say 4-5 days, than reboot and try it again if it lacks up and if your mouse and keyboard still works.
For some strange reason if you leave your system in sleep for overnight and do this for few days, the USB ports will starting to act up than your mouse and peripherals acting strange, try it and that is with USB 3 drivers installed, without the drivers installed all its good or if you just shot PC off than you won't or you might not know this behavior

bdary

AWK16

bdary
Still no issue's here with my mouse connected to a USB 3.0 port.  Booting, in & out of sleep often, gaming, and general use (6 - 8 hrs a day) without issue.

Are U on Win 10 or 7, sorry maybe you have mentioned somewhere earlier.
Do you put your system to sleep/hibernation, if you don't, try it for few days, say 4-5 days, than reboot and try it again if it lacks up and if your mouse and keyboard still works.
For some strange reason if you leave your system in sleep for overnight and do this for few days, the USB ports will starting to act up than your mouse and peripherals acting strange, try it and that is with USB 3 drivers installed, without the drivers installed all its good or if you just shot PC off than you won't or you might not know this behavior

I'm on Win10, and as I mentioned above, I use sleep multiple times a day with no issue's.  What I don't do is let it sleep overnight.  I shut down at the end of everyday.  I see no reason not to.  In this day & age when systems boot up in a matter of seconds, I see no point not to shut down when done for the day.

That's why I mentioned sleep mode and if you keep  your system ON during the day (with sleep mode here and there) but also if you keeping your system on sleep mode at night because that's where the USB 3 issues accrues.
You right, there would be no reason keeping PC on (sleep mode at night) especially with fast SSD's and overall fast systems this day, unless you doing other things like  for example, I do remote data collection from several systems all over Ontario and that happens at night, (50-100TB of data coming to my central server).
 
But anyways, if you leave your system ON for days and between sleep mode and actual ON state something happens with USB 3 ports, I don't know what I have been troubleshooting this fro very long time and if your system is ON long enough and that also could happen within day or two or week as soon as you connect anything to USB 3 it starting to lack up/freeze and on occasions while entering sleep mode PC hangs and there is noth8ing you can do unless U hard reboot.
 
I have been in touch with Gigabit and Asus about this for months and I can read between the lines and there is nothing you can do to prevent this strange behavior unless you do 1 of 2 things:
 
1. If you have USB 3 drivers on your x99, reboot your system once a day
2. shot down every night or if you lucky every other night
 
That's why many don't even know the issue because they either keep their systems ON at all times 24/7 or shot down at night.
 
I for once don't need USB 3 so no drivers, no issue here.
 
But I will agree with you, there is no need to keep system on 24/7 and let it sleep at night, there is no benefit unless you like me and have reason
 

I haven't had any problems with USB 3.0 in front or rear ports and I use them very frequently for a mix of 2.0 and 3.0 peripherals, portable drives, backup, phone, camera, and gps.  No issues with sleep, either.
 
I have run this computer with Windows Pro 7, 8.1 and 10.  No USB issues with the brief experiments in Linux Mint either.
 
Only issue I've ever had problems with is a WD MyBook drive which is flaky in everything I've plugged it in to - I've been blaming the power cord, not the USB cable.
 
Sorry this isn't very helpful, but wanted to let folks know I haven't seen this problem.
 

I don't use SpeedFan. I water cool my system and use a hardware fan controller for my radiator. Case fans that are plugged into the motherboard have a set speed in the bios.