I saw some mention earlier about the fact that there are problems with the USB on / off functionality built into gmenu2x.
The icons run the scripts usbon.sh and usboff.sh in <gmenu2x home>/scripts .
The problem is that, doing it this way, you can connect to your computer, copy stuff over, disconnect and all your changes are gone on the GP2X. If you moved files (rather than copying) then they'll be gone from your computer, and they won't show on the GP2X.
My theory is that, as both the host and the GP2X are intelligent devices, we have a contention of filesystems - the GP2X thinks it knows what's on the filesystem, but something else has changed it behind its back (and knows it has!).
The "sync" command won't help (as was previously suggested) because it simply causes the GP2X's version of the filesystem to be flushed to disk - not the computer's version.
I've found that if, after doing your copy or whatever, you do a umount /mnt/sd and then mount /mnt/sd (from the GP2X command line), this seems to get rid of the problem, and the missing files appear. By doing this we are forcing the GP2X to take a clean view of the filesystem, which supports the theory.
Ryo, not sure - can this be incorporated into the scripts? Might be a bit hard as gmenu2x is probably running from the volume we are trying to unmount. Might need to chain the script...