Emulator

What steps will reproduce the problem?

1. Open Dolphin, Play a game. (OTHER than Metroid Prime or Metroid Prime 2)
2. End Emulation, but don't close Dolphin
3. Start Metroid Prime 2 or Metroid Prime

What is the expected output? What do you see instead?
Expected to see ANYTHING... In Metroid Prime 2, it's a completely blank screen, however, the emulation is still taking place, sound works, I can hear it when I do a menu change, etc.
However, In Metroid Prime 1, I get Unknown Opcode errors, and the game then does not work and I get 0 FPS and over 11000 VPS (Speed 18000 %)

Dolphin version with the problem? Other Dolphin version without the
problem?
r6800 r6806 both have this issue, As to when it started happening, I can't say. What I can say is that if I close Dolphin (and wait for it to crash on exit, because it does that too, but that's another issue) Then re-open and run the game it works just fine... Something is obviously not getting cleared right...

32-bit or 64-bit and any other build parameters?
64-bit, no special build, I compile my own, and also tried Mamario's builds, no difference.

OS version and versions of tools/libraries used?
Windows 7 64 bit. Using ANY Plugin combination. OGL, DX9, DX11, HLE and LLE alike..

Please provide any additional information below.
This could be related to issue 3694... If so, please merge. Just reporting it as it could help to track down the problem..

In testing, I noticed that if the first game you start is Metroid Prime 1 or Metroid Prime 2, it works no problem. It's when you start a Different game then start One of those Two games that the problem happens...