I’ve found the same problem…. when I export (to QT/mov) I’m very sure that the alpha was set to ‘straight’ in the past and it worked fine. Now the preview window looks fine, but any opacity settings seem to be ignored when exporting. (eg. a ‘fade-in’ doesn’t fade, but rather simply ‘jumps’ from 0 to 100)
I found I could fix the problem (eg. create the correct opacity changes) by setting the alpha to ‘premulti Black’ rather than ‘straight’ (still exporting to QT).
Although the exported .mov has a “black” background, it becomes a correct (transparent) alpha-channel when it’s dropped on the Premiere timeline.
Hope this helps…Rob