My general setup is Windows 7 64 Pro on an SSD, all other data on normal spinning SATA disks. Seems similar 
For me CCCP/MPC works like a charm.
Try desperate measures like deinstalling player, then use CCCP Insurgent, follow up with cleaning the registry, check manually for installation remnants in Program Files, etc. Then reinstall CCCP off the shelf...
If that does not help, I'd make a hard reformat of the system. It just should work.
Sorry for the double post but I believe I found a fix, this may be of epic proportions
As I intently noticed every detail it took to recreate the problem, I noticed I use ccleaner a lot, even between playback (I live by ccleaner, been using it for as long as I can remember) and then I close the windows explorer window containing the mkv files and close mpchc. Then since ccleaner would delete cache files, the mkv icon's and all the other folders will reload and recreate some of those files, but restarting my rig recreates all those files hence why the problem doesn't exist once I restart.
Once I boot up and then not run ccleaner to delete those cumulative files that I'm used to deleting, subtitles load for every file without fail, no matter how much I try. So I check ccleaner to check the contents it was deleting, and I notice it was deleting "C:\Users\Administrator\AppData\Roaming\Media Player Classic\default.mpcpl". CCleaner was the culprit this entire time. I spent so much time reinstalling mpc, trying different codecs, fiddled with all the possible settings.....
tl;dl
Don't use ccleaner while using mpchc.