Uh, I've never had that problem. However, what happens to me often is that the settings I had set five minutes ago were not properly saved when Dolphin had exited so I fire it up again I notice a weird change in framerates. Check your settings each time you start Dolphin to make sure they were the same that you set last time.
Windows 7 RC Build 7100 x64 || Windows Vista SP2 x64
Intel Core 2 Duo E8500 (3.16Ghz)
ATI Radeon HD 4870 512MB (750Mhz/900Mhz)
OCZ Vista Gold 4GB RAM (2x2GB) DDR2-800
Asus P5QL-E
OCZ GameXStream 600W
Intel Core 2 Duo E8500 (3.16Ghz)
ATI Radeon HD 4870 512MB (750Mhz/900Mhz)
OCZ Vista Gold 4GB RAM (2x2GB) DDR2-800
Asus P5QL-E
OCZ GameXStream 600W
