Out of curiosity, could you try another setting as well? Four threads instead of two, but lower max cpu utilization a bit.
Well, I've largely switched over from PrimeGrid to NumberFields on that box now, but I tried setting it to use 100% of processors (all four threads), and 90% CPU usage.
Now, it doesn't actually hold the CPU usage at 90%, it kind of modulates it, and I see it skipping between 1%, 30%, 60%, and 100% fairly regularly.
Regardless, my window minimization doesn't seem to be affected any more.
Edit: I guess I ran out of GPU compute WUs too.