The flickering could be from an interlacing issue. It could be the effect itself has a bug in the Matrox plugin. Have you tried to chat about it in their group discussions? Otherwise here are a couple of work around ideas:
-If you have the RT.x2 you should be able to hook up a tv to the PPro timeline in the output breakout box. Use that as your guide to how the effect is working.
– Matrox has WYSIWYG technology so if you are seeing it happen through a monitor connected to the breakout box from PPro timeline it will most likely be there on export.
– Is it a Matrox effect? Or PPro? Try one then the other to see if they both have the same problem.
– Blur the clip that is transitioned (got the problem) just a little. As a test.
– Deinterlace the parts of the clips that have the transition applied to them.
– make the effect shorter. See if speeding it up makes it less noticeable.
– Matrox used to have it’s own encoding interface for MPEG-2, it was under export to matrox… Try that for the encode.
If none of this helps, tell me what your clips info is:
frame rate, tranistion type/length, DV/HDV, Project info (like frame rate, field domination (upper/lower), PAL/NTSC. Speed changes? Is it part of a nested sequence.
Cheers, Jon Barrie