I had to kill all the sessions that were stored in folders on our server, because they were eating up all our disk space. But... why exactly that would mess with the cookies is beyond me. I believe it would, but I'm not sure what the mechanism behind that is. Bah! What a pain. 
I hope that sorts it out for you, at least.
Gotta love computers sometimes, eh? I swear they do stuff like that, which doesn't make sense, entirely on purpose just to see what you do. And then they use the results as data for their eventual world takeover. Like Robotron 2084 except without the evil fire hydrants, probably.
