AME Exported Videos show transparency differently than when viewed in Premiere Pro!

Question

This is kind of hard to explain but basically AME does not seem to treat 99% opaque as 99%...instead the exported file looks more like 90-95% opaque. If you have 2 clips (contrasting clips are easier to notice) on top of each other in Premiere and the top clip is at 99% opaque and the clip beneath it is at 100%, in Premiere you can hardly see the bottom clip, if at all. At 99%, that's how it should be. Just barely peeking through the top clip...
BUT...
If you export that clip using AME, the resulting clip will look completely different and it looks more like you had the top clip set at 90-95%. The lower clip is MUCH more visible. There is not "barely peeking through" like you see on Premiere. It appears that AME does not handle transparency well. For example if you cross dissolve two clips. It looks fine in Premiere but export it out to Bluray/DVD, etc. and all of a sudden, sometimes the beginnings and ends of the clip abruptly clip on or off as they fade into the clip. Again, it's like they go from 5% to 95% but miss out on the subtle start of 1-5% and the subtle ending of 95-99%.
There is a thread about this in the Premiere section but I figured I'd toss it here since it seems Premiere handles/shows the transparency perfectly, but the issue arises when it's exported. To really define the point see the following clip that another user posted in that thread I just mentioned. Notice how the cross dissolves abruptly start and end sometimes. I noticed this in my exported videos too because I use LOTS of cross dissolves. It's easier to notice on more contrasted clips, but I think this illustrates the issue really well.
https://vimeo.com/14536285
Again, I just edited a project that had 2 clips stacked on top of each other and I accidentally had the top clip at 99%. I didn't even notice it in Premiere. You really cannot see the bottom layer peeking through...well, barely. But it's really subtle which makes sense because the top layer is at 99%. But on my exported Bluray/DVD...holy cow, it's VERY noticable! Almost as if the top clip were at 90%, not 99 (no exaggeration).
I don't see a BUG Report for Adobe Media Encoder so I submitted a bug report in Premiere Pro.
Can any one (staff preferably) address this issue please?

Answer 1

Thanks for the response Todd. Is there a way to get around this GPU vs. CPU thing you mentioned? If not, is there a way to export from Premiere (to DVD/Bluray/Vimeo H.264) without using Adobe Media Encoder or export somehow so that dissolves and opacity changes are handled the same way that Premiere handles them so that the exported video doesn't look suddenly different? (I'm on a 2011 iMac with 16gb RAM and the AMD Radeon 6970M Graphics Processor) Basically, am I screwed and there's no current way having these issues with transparency that I mentioned above?
Here, by the way, is the thread I mentioned that has to do with cross dissolves. I figured it was just an issue with that specific transition until I just now did this export with a 99% opaque clip on top of another clip and the resulting export looks more like an 85-90% opaque clip.
http://forums.adobe.com/thread/898211?tstart=0
Thanks Todd!