animations misaligned during preview/publish

I'm using Presenter 09, I've never had this issue before. 

I've got a series of shapes that lay on top of each other and fade out/reveal at certain stages. 

I'm finding that even before any animation begins the shapes are misaligned. The timing of actual animations to the audio is fine. 

I've tried grouping the shapes AND saving as a single picture .jpg. 

Also, any "transparency" animation turns it to a different color in preview/publish. 

I haven't searched that list yet, but possibly transparency as an animation not supported by Articulate???

No real help. 

Any ideas?

Cheers

Aaron