Pocket PC Weirdness

Anybody out there know of any issues with the Pocket PC misbehaving when you try to sync files up with a desktop or laptop? The behavior I have been seeing is that if I've been editing a file on the handheld and I try to sync the handheld up with my laptop, then the file gets copied up to the laptop but then it gets deleted for no apparent reason. The file is still on the handheld. If I go do a trivial edit on the thing and then sync again, the file comes back. But for no reason I can discern, it's tossing versions of these files when they sync up.

I've been poking around the Microsoft Knowledge Base, but so far no luck finding anything up there about this behavior.