Egads.. It's the Blackmagic Drivers for the Intensity Shuttle themselves.
After successfully playing back the sample vid on several other boxes I started getting this box in question back to basics.
I removed the BM drivers and viola it's fine.
Re-install, issue is back.
This is with or without a Intensity Shuttle connected.
Now how they interfere is really crazy.
I've torn apart their driver install to see exactly what they are installing and tried various graphedit combinations and can't see where they jump in and mess this up.
In graphstudio the graph construction and events report are identical with/without the bm drivers installed yet render differently.
It's obviously not a MPC or MPC HC configuration issue at this point.
If anybody wants to try this and (hopefully) see what I'm seeing you can load the BM drivers without usb 3.0 or the intensity shuttle itself. They at least uninstall cleanly.
Edit - you don't need the full driver install
Here are 32bit and 64bit versions of the codec.
You can regsvr32 register/unregister through an Administrator Command Prompt to see the issue.