BAP, I clicked the Protection tab in MalwareBytes and it appears that the Shield-type protection you're referring to is called Realtime Proection Module and as you guessed, is in the Paid version. I've personally never found a shield-type thing worth the drain on system resources and have always disabled them. Note that most authorities would say that's bad advice. Nevertheless the default setting in Windows already run scads of that type of upfront protection (which I also disable and make authorities faint) 
Your call.
Anybody is free to get in here and give alternate advice on anything, I won't be offended! You tooooo, Micro!
Best thing I read in your note, BAP, is that folding continues to run. This is good. But the blinking cursor or windows or whatever it was persists? Makes me want to say BIOS, but that starts to get tricky. You could alternately run a memory test, never a bad idea anyway. Go to http://www.memtest86.com/download.htm and d/l either the usb or cd version. Making a bootable usb is probably easier than burning a bootable cd, but that's just me. Either way, whichever you choose will have to be in your machine boot sequence before the hard drive. That's a trip into BIOS under Boot Sequence when your machine is re-started if one of them isn't already there in sequence before the hard drive.
Sorry this isn't a little easier, I'm very tempted to say why don't you leave it all if folding is all that really matters on that machine. Your call though.
On the Titan, that's almost scandalous that that monster isn't folding! 
Is that what's plugged into the monitor for that machine and if so, is the video there just fine? That would indicate that the pcie slot is fine and so's the card, at least for both on a basic level. If that's the case, what driver version? We want 327.23 .
Some stuff for you consider, BAP, don't let this wreck/dominate your weekend, do it when you feel like it, or even not at all if you're uncomfortable with it, as I say I won't be offended.
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