Sorry for the late reply, was completely away from home all of yesterday and this morning.
The not starting problem seems to resolve itself.  It had something to do with using the Disk Cleanup utility that comes with Windows.  I turned on the "Clean up system files" option and there was about 6 GB of Windows Update files that were available to be deleted after it ran through its analysis. After doing that and restarting, my PC seemed confused.  Fortunately completely powering it off for the night worked and it now it starts up and I can use it normally.
The low FPS thing has not been corrected however, just tried out TF2 and it dipped below 10 frames per at a certain point.
I guess I need to do a reinstall of Windows, which could be a problem because I've moved twice since my last install and have no idea where the disc is. 

  Time to start my back ups.
Thanks for the tips so far everyone.  I'm guessing it will be a few days at the earliest before I can do the fresh install, but hopefully once I do, it clears up the problem.
KT
Edit: actually, not a huge deal since I have the majority of my stuff on my secondary TB drive and I just boot and launch games from my SSD. Not much to back up.