Since installing the P3300 patch I've still had filesystem issues, but instead of the filenames getting garbled and the outrageous file sizes and dates, here's what's happening: The directory structure remains intact, but the files vanish. Reset, and they're back.
I decided the best way to fix this is to go Blackberry. I like Windows Mobile, except for the fact I haven't yet come across a WM PDA or phone that works as intended. Combined with the fact HTC has had this issue before and still can't get it right (and my Touch is a replacement for several Mogul's that also didn't work right) I think it's time to call it quits and go back to what works.
