heh. I figured out that the 2 changes made ubb_pm did all the damage. It actually called ubb_folders and reinitalized already taken variables thus taking some out or putting the wrong values in. SO... i have applied the patch and so seems to be working great.
To those who is showing the deleted PM's, other PM's, there is a script located under the pmfolders zip file on the first post. Rename the txt file to cgi and run in your ubbcgi directory. It will essentially backup and recreate the pm files.
If you have not changed anything from the install yesterday, the only difference will be in ubb_folders.cgi and public_pm_folders_review.pl.
Either way, running the backup at least once will clean everything up. If you have a big board, it may seem slow abit.