(taken fomr a random forum thread with a quick google)
A FAT32 directory can have 65,536 directory entries. Each file and
subdirectory takes from two to thirteen entries, depending on the
length of its name, so those entries can disappear long before you
think you've used them all up. Your total of 22,657 files could very
easily use 65,000 entries.
so yeah, possible it's hit the limit if they're all in their own folders or something?
have you tried sorting them into folders for each letter? i can get all the megadrive roms on no problem (probably less though)