Hi Brian,
Please open a command prompt as an Administrator and type the following and then hit enter:
%windir%\debug\mrt.log
and copy/paste the last page or so of the results in your next reply.
It should look something like the following, but note the difference between the last 2 entries (red arrows + 1 to different text; note red arrow & 2 showing it took minutes (not seconds) to complete). That's sort of what I'm looking for:
Please see https://support.microsoft.com/en-us/kb/890830 and download this separate program and install it. Read the information. Please run if first in quick mode and then again in full mode. This is a way to manually run it on your system at your whim vs. "monthly" - though I'd consider it rarely needed - but should help us test a lot easier. When we're done, you can delete it if you wish.
Despite the "all clear" from the other programs you used, I suspect the root issue is either some infection or the remnant of an infection OR a problem with the most recent update/upgrade (or both). This download should help rule out the latter. Then we'll need to delve deeper into making sure your system is clear of all infections. But small steps so we don't get ahead of ourselves.
Hope this helps and please keep us informed.
Thanks,
Kosh