Not sure if this is related to you problem.

I also had a problem with my video clips being of different size, when there were effects and titles, but my picture became cliped/croped on the edge when there were a title or effect.

fortunately I found out that all I had to do was remove all the preview files, and then everything was fine. dont know if its done in the same way in Premier 6.5 as it is in Premier Pro.
In premier pro you select the sequence then under sequence in the menu bare, you can delete the pre-rendered files.

Hope this helps.