Hi there,
I'm evaluating Stereoplayer which works fine except for this issue.
However, I'm not convinced this is an AMD driver problem, because the issue isn't there (and has never been there) with any version of TMT or PowerDVD. Both software play 3D Bluray content on AMD (I have a 7870) using HD3D without this issue, which I immediately noticed on stereoplayer, without being aware of it. I only found this thread as I was looking to see if it was a known issue or not.
I've only tested 3D Bluray with both software, as while PowerDVD looks like it can read MVC mkvs it's only converting them from 2D to 3D (poorly!), and TMT can't read MVC mkvs.
But when reading an MVC mkv with stereoscopic player, the issue is there while it isn't there in a 3D Bluray played by TMT or PDVD.
Could there be a difference in the way you access the driver? More specifically, could it be a difference between unlicensed players and licensed players, and the way they are allowed to process the MVC stream?