I am having some issues with my X99 Classified based system, related to two separate USB devices - a Corsair K95 keyboard, and a set of flight pedals made by Slaw Devices. I don't know if these problems are related but they're both USB and seem similar, so I'm guessing there's a good change they are.
 
system specs - I'm just going to list what I have connected during my testing, if it's relevant I can provide the rest of it.
X99 Classified
5960X
32GB ram
3x Titan X SLI
SSD
Windows 7x64
cheapo Logitech keyboard
cheapo Logitech mouse
 
The motherboard is on 1.16, I've tried other versions 1.09, 1.12 and had the same problems.  For both devices I have tried a wide variety of settings - I just got off the phone with EVGA tech support and we went through everything.  I have the boot config set per this post in the 1.16 thread - http://forums.evga.com/BIOS-116-Released-m2304549.aspx#2309215 and i have fast boot disabled. Under the USB configuration, I have tried enabled/disabled for legacy, and all three settings for XHCI - smart, disabled, enabled.  
 
Problem #1 - I have a Corsair K95 keyboard that the motherboard does not enable/initialize correctly until Windows loads.  It simply doesn't work before I hit the login screen.  Occasionally when I get to the login, I have to unplug it and plug it back in to get it to work, but once it's working it's ok.  It's plugged into a single USB 3.0 port - for those who aren't familiar with it, it has two USB plugs which you use both of if you're on 2.0 ports, but only one on 3.0.  It doesn't make a difference as far as the keyboard working before Windows loads, whether I have one or two plugs connected, or on 2.0/3.0 USB ports.
 
Problem #2 - I have a set of flight pedals made by an individual in Poland, his one-man shop is called Slaw Devices - so obviously not a big name brand like Saitek or CH.  The pedals are a pretty standard 3-axis setup, and for other people work fine on both USB 2.0 and 3.0 ports.  For me, if I have them plugged into the motherboard at all, the computer will not boot - it hangs at the BIOS boot screen. The only exception to this is if I set the xHCI option to disabled - in this case, it will begin to load windows, I get the four-color swirl, as it comes together the computer reboots.  Any other combination in the BIOS just causes it to hang on the BIOS boot screen, with a code 'A2' at the bottom right. I have tried the pedals on two other computers, they boot fine and work perfectly, but neither has USB 3.0 ports to test.
 
I can plug in the pedals once Windows is booted, but unlike with the keyboard, I am seeing some problems once booted into windows with the pedals as well.  With xHCI enabled, the Game Controllers window is flaky - it hangs, doesn't respond for long periods of time, etc.  It's better with xHCI disabled, but I still see minor problems - testing is not smooth, in the Properties popup where you can see the axes move around as you move the pedals, occasionally there's minor hangs there with xHCI disabled as well. I have contacted the guy who built the set for more information on the USB controller in the pedals, hopefully I can get some information on what controller he uses to pass along.
 
As I mentioned, I spent 30-45 minutes with EVGA tech support (sorry, didn't catch the name) and we were unable to figure this out, it's really sounding like a BIOS problem with handling USB ports.

Your USB Devices are USB 2.0 so you should use the USB 2.0 Ports.

Testing with the newer drivers from Intel, no difference - I was hoping that perhaps it would be a little more stable in Windows.  Obviously these drivers don't make any difference to the fact that I can't boot with the pedals plugged in, that's a BIOS problem.

This looks to be an issue with those peripherals plugged in.  Hopefully they'll have a BIOS update for this in the future.  Big fan of watching other's flight simulating setups.

bsoder
Yep, I'm just leaving my controllers unplugged until it's booted up. Frustrating, but hopefully a BIOS update will fix it eventually.

On the bright side, I mostly figured out the K95. I still occasionally have to reconnect it at the windows login prompt, but using the BIOS switch lets me deal with BIOS and pre-windows stuff. Who would have thought a keyboard would need a BIOS mode...

I do the same, leave them all unplugged till I play something. It's not that big a deal but it would be nice for it to work right. I have TrackIR too and it doesn't seem to affect it at all. Only when the flight stick, throttle, and pedals are plugged in.

I get the same hang at bios with my Fanatec Club Sport v2 wheel base.   Fortunately, I only have to make sure it is off on computer startup.   
I have had similar experiences with USB extension cables and my mouse not working, but computer boots.  After many different cables I solved it with a powered USB 2.0 hub at the end of my extension.  
 

Even unplugging all the front panel USB's it is still freezing.  I just had to unplug the DK2 out of the rear panel USB 3.0 slot to get it to boot?!
 
I updated the bios when I got this board up and running less than a month ago.  Why is the USB initialization so shady on such a nice board?

This may be an old thread, but I see no definitive fixes and I am still having the issue.  I am on the 1.19 BIOS as well.  
 
I installed this mobo in my PC just before Christmas and it worked flawlessly for about a week.  Then I started getting these random startup freezes after the BIOS runs through the various hardware checks and attempts to pass the ball over to Windows 10.  It sits there until I unplug the USB which it is having an issue with.  My Oculus DK2 plugged in the back USB 3.0 panel was the latest freeze.  Started right up today though.  Very strange.  My Asus X99 Deluxe had strange USB issues like this too.  I always had great luck with EVGA boards, so I was hoping this Classy would get rid of all my issues.
 
Still runs like a champ once it gets past the USB initialization issues.

Are you using USB legacy mode in BIOS?
 
If your hardware loads software at startup in Windows - set it to delay those items on Windows startup.

bigweamer
Thank you for the suggestions!
I am on windows 10 and there are no official win 10 USB drivers yet, so that could be the issue.  I had the latest windows 7 drivers prior to updating, if that makes a difference.
My USB mode should be whatever the BIOS default was, I didn't mess with it at all.
Computer started right up today without issue.  As long as it keeps working like this I am fine.  If it happens to hang I unplug the DK2 and it starts right up.  Absolutely no issues in the OS or games.

Ok.  I only added the USB 3.0 driver link above because your sig shows you're running Win7.  Win10 doesn't require any special driver.

Very sorry about the sig bdary!  Updated to Win 10 (thought I had done that when I updated my OS but must have missed this forum)
 
I found the USB Legacy support setting and disabled it.  First boot worked fine and I will report if I have any issues in the future.
 
Thanks again for the help!

bigweamer
 
I found the USB Legacy support setting and disabled it.  First boot worked fine and I will report if I have any issues in the future.
 
Thanks again for the help!

Always glad to help other forum members. 
 
Give us an update in a couple of days.
 
 
Enjoy your Build.

bummer .... thought you were in the clear

Three freezes in a row now with my CH products plugged in the front panel USB's.  This time I unplugged the throttle first, but it didn't load windows until I unplugged the CH Fighterstick as well (the issue must not be tied to a certain peripheral).  USB Legacy support was still disabled.  My BIOS settings are saving as they should.
 
Seems like a really stable XMP 1 setting so I hate to change it just for this strange USB hangup. Everything else is working top notch.  Here's hoping for some better USB drivers for Windows 10.
 
It is doing awesome in benchmarks.  Just got a 15541 in FireStrike and 41660 on the Skydiver (better than 99% of all results ).  Runs perfect the entire time it is on.  Only issue is the strange USB hangups on startup.

Glad you found an answer that seems to stick
 
Is that a USB 3.0 device?