--- Operating System, Graphics card ---
The issue is reproducible with windows and linux. No other OS available for testing
--- Blender version with error, and version that worked ---
It works properly with Blender Release 2.65a
It does not work with Blender Release 2.66. I have also tried the RC, with the same bad result.
--- Short description of error ---
It seems to me, the problem is connected with the new "Image Transparancy".
In VSE, If you SUBSTRACT one picture by another, the the result is all black, instead having a new calculated image.
--- Steps for others to reproduce the error (preferably based on attached .blend file) ---
In the attached .7z file you will find a .blend file, which shows the issue. You will also find a good_case.png showing the expected result and a bad_case.png showing the issue. The only difference between Blender Release 2.56a and 2.66 is the disappeared "Premultiply" button. If I check this button in 2.56a, then I see the same bad result as with 2.66.
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This was actually a display issue -- sequencer in 2.66 was actually displaying RGBA image, and in previous versions it was more like RGB image.
I've added a way to display either RGBA or RGBA in the sequencer in svn rev54904 and think it shall solve your issue. There're still some improvements to be doe, but that change shall make sequencer behaving closer to render result in image editor.
Thanks for the report, closing.