Not much of an answer for you from me Im afraid,
But did you use the same HDMI spec cable in your tests and I take it both PS3 and HTPC were hooked up to the same display?
My set up is on a 46" LED but only having tried a couple of 3D movies, one of my first was the latest Haryy Potter.
I was watching it on my 3D bluray player and it looked crap.
I put it in my HTPC and it looked just as crap.
The HTPC has an AMD 6770 in it but I dont think i tried playing with TMT5 depth settings to see if anything changes. I'll try it tonight.
One thing that did happen with TMT5 an 3D bluray was that if I skipped forward the audio (set to bitstream) would crap out.
PDVD 11 worked much better but the way that TMT5 recognises a 3D bluray is much better than PDVD 11. Its not automtaic in PDVD11 and setting has to be changed manualy in the UI.
Unfortunatley, I read the reviews of this Harry P 3D bluray after I bought it and even the reviews said it was crap.