I believe I have a work around that is allowing me to use both Compressor 4.1 and the Matrox compressHD card.
I went and deleted all of the preference files and move all of the Application Support files to my desktop for safe keeping, and deleted and reinstalled 4.1 so it was as clean of an install as I could make it. Then, rather than trying to install the old Matrox presets, I created a new custom preset in Compressor. In the Video -> Quicktime settings section, I chose Matrox MAX h.264 as my codec.
Voila! My new preset is now working like a champ using the Matrox compressor. I’ve encoded several files, testing with and without, and it is definitely working! Encodes are taking place in ~real-time, as they were before the upgrade.
It is annoying that all the old presets don’t work, but at least this is a bit of a work around that seems to be solid until Matrox updates their product.