Jim,
I don't have any virus software installed. I did a clean Win7 install last weekend and have not installed anything. However, I did allow Windows to install "all" the updates (100s of GBs of file changes) - and it wouldn't be the first time a Windows update broke something. Now that i think about it, I might just start over with a another new Win install but not allow any updates (other than absolutely required). Usually I turn off "Windows Updates" on my HTPCs since i don't use them for anything but HTPC duty (most of Windows updates seem to be fixing a security or compatiblity issue anyway). So if it ain't broke don't fix it.
Regarding resources, I would expect CPU/GPU or memory use to be high if it were a resource issue. My CPU, GPU, and Memory loads are all below 5% (if the Windows Resource Manager is reporting correctly).
The problem is not occuing on every BD movie I play - so finding what fixes it and what does not, it difficult. I make a change, start a movie it looks good - I think the problem is fixed - then later I try watching something else and it freezes - so problem not fixed.
Seeing that I have flawless MadVR playback on my other HTPC (and it is weaker CPU and video card), I know the problem is not with MC16. I am only posting here to ask for ideas.
I will look through your Weird Problems listing too. Possibly the solution to my problem will make your list too.