Hmm, this used to happen a lot to me when I was devving for the iPod linux project (different device, same stuff, mainly...) sometimes I would unplug the iPod without ejecting it first, a real bad idea when using any Linux distro I know of
It left me with 2 folders that filled my measly 1 gig iPod right up, making even a restore using the iPod updater impossible.
The first time it happened I simply ran a chkdsk (Start, Run, CMD, chkdsk X: /p where X: is your NAND) in Windows 2000 on the device, and voila, I could delete the folders, and all the data that got shoved into the FOUND.000* folders. The second and subsequential times that it happened chkdsk did not work, even fsck.vfat didn't help. The only option left was to format the file system. This is a lot easier for you that it is for an iPod, as theres a utility (as mentioned in the first reply) built into the GP2X to format the user area of the NAND. Make sure you have a good set of batterys in (you really don't want them to cut out!) Goto Setting --> System -- NAND --> Format = Yes and press B, the NAND will format itself (it only does the user area, don't be scared!). If that *really* does not work, you will need to get the HP USB Format tool (google it). If it can format a busted filesystem on a hacked iPod, I'm sure it can format the GP2X NAND
Good luck!