Did the FPS cap, or anything else, make a difference in the frequency this would happen?
Unfortunately I don't recall anyone else reporting this problem, and the things that were close you've already tried the relevant troubleshooting.
Try doing a clean boot and then test the game (maybe create a new Windows administrator user account, and log in to that account after rebooting). Click Start, or hit WinKey-R, type in msconfig and hit enter; in the General tab, click Selective Startup, uncheck Load startup items (if required) and leave Load system services and Use original boot configuration options checked. Next, Click on the Services tab, check the box to Hide all Microsoft services, then click the Disable All button, then click OK and reboot the computer.
Run msconfig again to switch back to the normal boot configuration.