Another possibility, since you are using an SD card. SD cards have a limit to the number of files that can be stored in one directory. When you hit the limit depends on the length of the file names. I would be surprised if you hit the limit with only 2500 files, but it could happen.
Also, SD cards get *very very* slow when a lot of files are in a directory. See the FAQ
I have added a lot of books on an SD card and now downloading books takes forever. What do I do? for more information.