I have a very similar issue on one of the 2 PCs that I use. I've checked each gamepad on each machine. Both work fine on one machine and both 'disappear' for brief moments randomly on the other. When they disappear whatever action I may have been doing is repeated rapidly for ~5 seconds. So I either continue running in one direction, the camera spins, I repeatedly open/ close the map, etc. When the controller comes back, all gamepad settings will be reset to however I had them when I booted up the game (meaning to actually change controller settings I have to immediately log off after, otherwise they revert). The machine this happens to me on is running Win 8.1, all drivers up to date, etc.

From what I could tell looking around this seems to affect a small number of people and has been going on for as long as 5 months or so. I've yet to see anyone post about fixing this problem except when it occurs with PS3 controllers, though I think that's probably just a similar but unrelated issue.