The listfiles example will fail if you have more than 26 files because it fails to close the files and you run out of file handles. I discovered this, not by having too many files, but by rewinding the directory as I was scrolling through the files with an LCD GUI.
It's a simple fix, just make sure you close the files when iterating over a directory.
I filed a bug: http://code.google.com/p/arduino/issues/detail?id=832 and the fixed example is: http://arduino.googlecode.com/issues/attachment?aid=8320000000&name=listfiles.ino&token=MA2OkD4QfvBFDY9sk_S6aeM9Cwo%3A1330552643785
I also did a pull to the adafruit repository version, but I'm not sure if that's active because there's been no response.