I was wondering if there are USB issues with X99 as I have been battling this mouse issue for about 3 years or more, over several different mice. 
It's a bit random, and took me this much time to pinpoint the issue. or I think I may have anyway.
 
So I boot up Windows (Currently 1909 up to date) 
Mouse works fine, feels very smooth and easy to control. 
after a bit, or sometimes when I open a program, maybe Email, or Steam, or anything my mouse cursor feels janky, almost like the DPI was turned up, but more so that the Polling rate has dropped from 1000 to 125. 
 
The way it get to back to normal is open Logitech G-Hub, or Windows mouse settings, and just toggle settings. what seems to work best is toggling the polling rate to 125, and back to 1000. 
This is only temporary as its back to crap in a few minutes or so.
 
Over the years I have searched and cannot find anything until recently I find it may be the USB ports.
Have I been dealing with this problem and it's the motherboard all these years? IDK
 
Any ideas what the problem might be?, as I cannot prove this is the issue.
But I's made me want to just quit the PC completely It is very annoying and unsettling sometimes can't even close a window. or put a cursor into a box, or select text.
Needing to make precise clicks is almost impossible until I do the temporary fix.
 
Mouse: Any mouse. Logitech G703 Lightspeed. (other mice I've tried G502, G700S, cheap Microsoft, Logitech, and Corsair mice Wired, and Wireless)
Motherboard: EVGA X99 FTW 
Windows 10 1909, and several previous 
EVGA RTX 2080 XC2 Ultra 
G-Sync Compatible ON ASUS VG278Q X (2) 144Hz
 
I've tried different USB ports, Wired, and Wireless, USB3.0 & 2.0 
turned off all RGB and other functions not needed. it does this with any mouse I use. 
I've tried onboard memory, as well as PC
 
I hope maybe someone has some info on these anomalies 
 
Thanks for reading.
 

I know i'm not using the latest bios as the newer ones had some serious performance issues. 
My OS drive is on M.2 PCIe, so no cables, but I have had this issue on a SATA 850 PRO as well as hard drives. several OS installs over the years. 
 
I am running 3200MHZ XMP 32GB ram.  
No overclocks on anything else.
 
Since I have double BIOS I will will switch over and do BIOS update to 2.08, and set ram to 2133 stock. 
 
Also to note I have 12 drives hooked up on here I wonder if that will cause an issue. 
2 NVMe on PCIe, 1 SATA SSD, 5 HDD RAID 0, 4 HDDs 
Also all PCIe is populated except shared GPU. 5 PCIe devices.
 
Thanks, I will test the suggestions. 

So...you unplugged the other devices and tested?

Or not, and just had them powered off? Because you should test with them unplugged - including the keyboard at first.

I will say the 2.08 BIOS is not showing the performance loss it was with previous BIOS after Specter Meltdown
 

mr_scary
Well I've tested this for quite a while with the new BIOS. 
Still having issues. 
 
Mainly while selecting text to copy, the mouse will lag out, and only get partial copy. 
 
I will have to really investigate this. 
- Mouse gets hung up, and lags out.
- I see the desktop refresh itself.
- The mouse cursor gets re-centered on the screen. 
- Drag & Drop issues where I cannot grab a file and move it. takes sometimes 3 or 4 tries
- All sorts of issues like this.
 
I can try unplugging everything but the mouse, but I really think its going to keep doing this.  
If I have time tomorrow I will unplug everything but the mouse and start the PC. and test it for a while. 

When this happens, have you looked in the Event Viewer in Administrative Tools  to see if you're getting a display timeout or other error?

Funny thing I was trying to make a snip of the event viewer and it kept cutting me off before selecting the snip. 
nothing in event viewer for that anomaly. 
 
However the one that seems consistent is "Audit Success" every couple of minutes.