You may run into issues. You won't have any Matrox presets or effects available in CS6, and when you open the project PP is going to notice that.
Will the actual Matrox AVIs playback and edit without a hitch in CS6 without Matrox loaded? I know they're different than standard Windows AVI's. I've enountered stutters in 6 and don't know if it's my computer (or how I installed some new drives, etc.) or the AVIs I digitized in Matrox. It's a dual quad core Xeon and I've never encountered stutters before. I just want to make sure the source material with the Matrox I created will be stable if I need to make changes to programs down the line. Effects are not a problem.
Assuming DV, the files themselves should play fine.