Well I’m new to AE so I did not understand a half of the stuff in your file. I have tested your file.
However It seems to have problem now removing any small dirt. The dirt is black. See this screen shot:

Also for some reason I have a border around my image, tried to remove it to no avail. See this screen shot:

And lastly why does AE crash more often if I try to work and replace my footage than create everything from scratch?
I use Autocolor, FilmFix, Neat Video plugins. Is there any compatibility issues? My AE is latest CS3 v8.0.2, FilmFix is last version and NeatVideo is I thing v2.2.2