I have a problem similar to what is described at "Why is my USB mouse disconnecting and reconnecting randomly and often?" except is is happening in both Windows 7 and Linux (Ubuntu 12/04TLS, fully patched), multiple mice, multiple OSs. It stops responding to input for about 3-5 seconds, then starts responding again. It's more frequent and lasts longer when running games (TF2, L4D, Dishonored, Borderlands 2, and more), but happens when just running the OS as well.
I was hoping it was the motherboard so I bought a USB 2.0 PCI card to try that, but it's still happening. I've stripped it down to just the keyboard and mouse (different keyboard too just in case the keyboard was the problem), but it's still happening. All the hardware (mice and keyboards) work fine on other computers. I have literally pulled the mouse and keyboard out and plugged them into another computer (laptop) and re-joined the online game and had no problem with the keyboard and mouse combo that just failed on my gaming rig.
Please no driver / Windows or Linux only suggestions, as that wouldn't effect both OSs.
edit: known good mice I've brought home are now going bad. I suspect the hardware is messed up (voltage?) and has been frying the mice.