I did a little more testing on the WMP bug.
It seems like the bug only appears under these circumstances:
A) It only happens when using MT with either LimitedSharpen or the RemoveGrain.RemoveDirt filter. FFT3DFilter doesn't cause these problems with MT.
B)It only occurs when using SetMTmode. Using the old MT.dll causes no issues with any of the 3 filters.
C) It only occurs when I exit WMP without pressing the "Stop" button.
As long as I press the "Stop" button then exit everything is fine.
I guess I'm just more impatient than most people
.
This bug seems to be different than the FFT3DGPU one. But fortunately it can be avoided for now.
EDIT
Yes. Mplayer2.exe is the WMP program in the taskbar.