Slowdown even though game is at full speed!

[Dolemub42]

Regardless of whether I use OpenGL or Direct3D I have a problem in some games, like Metroid Prime 2/3 and Super Mario Galaxy, where Dolphin indicates that the game is running at full speed, and the sound is not crackling or slowing down, but the game looks and "feels" like it is running at 30 FPS or less. Sometimes this is temporary, sometimes permanent BUT it is always fixed if I go from fullscreen mode to windowed mode and then back to fullscreen mode.

Does anyone have any idea what this is or how to fix it?