There's a known issue with the file system routines on any official firmware 3.80 or higher. I'm running a phat PSP with 3.52M33-4, so I don't know a lot more about it (but I'm picking up on it as I go) except that the standard homebrew fix is to use the module from version 3.71. I don't know if it has to be downloaded separately or if it comes with recent custom firmware, but it can be configured from the recovery menu. That's all I know at the moment, I'm sure you can take it from there and find more in the forums or on Google.
You might want to plug it into a separate card reader and run chkdsk on it to see if the file system is ok.
2 Phat PSPs: First went through hell, reassembled scrap parts from 2 bad PSPs. Second is practically new except a repaired battery clip, both running 3.52 M33-4, first clean install, second modded. No, not planning to upgrade either.