Hi Artistdomain...
I'm wondering if it's the same issue that many other users have experienced with cross dissolves (search forum for "Cross Dissolve NOT smooth" for the thread). Can you somehow pull out and post short samples of the different cross dissolves or describe what you mean by "not as smooth"? In my recent post of the top 15 things I hoped the NEXT release of PPro would fix/add this issue is definitely one of them. See #13 on my list here: http://forums.adobe.com/thread/1179004
Is that similar to what you experienced? I'm hoping that the issue will be fixed as suggested by a SteveHoeg in post #32 of that thread. Let's hope we're talking about the same thing. I never dynamic link PPro to Encore so I don't think it's that...IF we are talking about the same "not smooth" issue.