Actually, I've had some of the problems you're describing with the auto-run & being unable to do things briefly. I have a wired XBox 360 Windows controller & have used it since 2.2 with no issues until recently (3.35-ish). It can cause panic if I suddenly auto-run towards something deadly!

It should be noted that it isn't the auto-run feature that is being initiated either, just a weird command from the controller. It started when they introduced support for the Dual Shock system. I've not updated any drives or software for the controller knowingly.