Got it. Try this super-simple test questionnaire. It's basically an instruction screen followed by a movie with no parameters at all. That's it. This will simply help us rule out any explanations that have to do with the content of your experiment.
To test it, rename one of your .wmv clips "test.wmv" and put it in the same folder with this que file (after unzipping it!). Run the clipTest.que questionnaire and see if the test clip plays ok or if you get the same problem as before.