I think you've got two solutions right there. General wisdom is to only work on new projects in the new version. Finish old projects in the version they were started in.
This is why.
Fair enough. Was hoping to understand the problem deeper in case different variations of it cropped up, but hopefully it's purely a conversion issue and won't bug us once all of our 5.5 projects are finished.
Is Premiere Pro CC updated to 7.0.1? This may fix these issues.
Yeah 7.0.1 (105)