Quicktime Flip - Copy and Paste

I am working on a script that combines several QT files into one, and am running into the following problem - I need one of the movies to be flipped over when it is added to the combined movie, and my flip/copy/paste method isn’t working.

If I manually open the Movie Properties, select the Video Track and flip it, it copies and pastes correctly. If I do this with the “Flip Vertical” or “Flip Horizontal” commands then copy and paste, the flip is lost.

So I am having to pause my script, flip the movie manually, then continue. Any thoughts on how this could be made to work?