I would test both of those issues. Are you looping the play all/playlist?
I wonder if you are running in VTS limits per disk. Encore uses auto-VTS, which means one timeline = 1 VTS. Limit of 99 VTS per disk. I don't know which of your objects get defined that way. I do not think each transition does (it is an asset, not a timeline), but you can get odd results with atypical violations of specs.