I have also seen this behaviour many times, both with 3.2 final and the latest 2 betas. It always happens when I have a LOT of files to upload and I leave the computer alone for 30 minutes or so to upload.
I do not have any screen saver active so I know that's not it. That was my first thought
Typically what happens is I will try to come back and FlashFXP is frozen. Sometimes I can get the window open, and even view most of the window, but the queue frame is completely white and never redraws.
When I go into Task Manager and look at it, it says that FlashFXP is using 80-100% CPU, so I kill it.
As soon as I do that, everything in Windows freezes. If I can ctl+alt+delete and get Task Manager open again, it shows that explorer.exe is using 80-100% CPU now.
Killing explorer.exe sometimes fixes it, but usually it doesn't and the computer has to be restarted.
Suggestion: my suggestion to reproduce this bug is to just start uploading a massive list of files (make sure that there are lots of subfolders and files within those subfolders) and let it sit for at least 45 minutes and see if it happens.
Thanks!
-Kevin