It seems that it might have something to do with very long file names, but Flash FXP will hang when you're scrolling through the directory. It doesn't matter if it's the local directory or the remote directory, it will just hang.
You get a windows hourglass, and you can't do a thing with the program. All it says is "Not Responding" and all you can do is shut it down. It seems to be exacerbated if you scroll quickly I noticed too.