I have the exact same problem on my running programs!
This is definately a Vista SP1 issue... I tried copying the currenttheme.ini and settings.ini file to my XP machine and the dock doesn't have a problem. I also tried vice versa and it didn't solve the issue.
I never had this error happen when I was running Vista without SP1, so I think it has to be Vista SP1.
I've tried reinstalling Stardock, deleting and reloading all my icons, lookin far and wide on google... nothing.
The problem occurs most for windows explorer windows, screen saver, and microsoft outlook for me.

Most of the missing icons below resulted after I mapped a few network drives and closed the windows.