Did you actually render out the transition & import the new file into PP, or are you using Dynamic link?
Personally, I wouldn't use Dynamic Link.
Are you using (standard) "Fill" or are you using "Eyedropper Fill"?
Are both your Pr and Ae versions within the same cycle?
What is your workflow for getting the After Effects composition into Pr? Are you importing it?
Dynamic Link works really well for many of our projects.
Are you still facing this problem? If not, let us know how you solved it. If so, please let us know so we can assist you further.