I apologize for not answering your post sooner!
It sounds like ViddyUp! is not picking up the pixel aspect ratio atom from your reference movie. Would you create a small sample DV50 file and reference movie, make sure the reference movie doesn't work correctly in ViddyUp!, then send both files to us so we can duplicate the issue here? The best place to send the test files is
support@splasm.com, with a reference to this forum post in the subject or body of the message. We'll figure out the issue and let you know what we find.