I use the Windows 7 task manager and Real Temp. Both claim 100% load at all times. I have tried setting it back to 50% and restarting, but that didn't work either.

Let's control for some variables then:
1) Help...About Prime95(or Prime64) reveals you are running what version, exactly?
And when you ask your system what version of Windows 7 you are running, what is reported?
2) If you run task manager, and Workers/Pause, and pause all workers, what does the CPU usage drop to?
3) Let's try Throttle=10 and see what that does...in particular, what proportion of the CPU time is Prime64/Prime95, as being reported on the process list in Task Manager?

If 2 doesn't work, it's probably not P95...maybe someone is mining bitcoin on your system...
If 3 doesn't work, but 2 does, it's time to ask Mr Woltman (aka Prime95) what's up....but the answers to #1 will be required.

It occurred to me after the last post that your method of stoppoing Prime95 might not actually exit and re-start the program the way you think. There's a bunch of little hazards there....like the red X in the corner just minimises or disappears the Prime95 window, it doesn't actually stop P95 from working.

I'm failry sure that P95 will actually exit if you stop all workers first, then test...exit.