I can't pinpoint the exact cause, but I uninstalled a bunch of software, and cleaned the registry, and reinstalled the Visual C++ runtimes, and the problem appears to have went away on Windows 10. One of those programs I had installed did something to the registry that Citra doesn't agree with. I suspect it may have been radeonpro, system explorer, MSI afterburner, or rivatuner causing it, but I can't be 100% sure on that. I uninstalled all those and cleaned their registry entries. So if anyone else runs into a similar problem with Citra locking FPS lower than it should be, you should look at similar types of software on your PC that I listed.
Last edited by crimsonedge11,