Specifically, which games are you trying to play in Dolphin? Have you tried the latest development revision (currently 4.0-318 as of this writing)? Additionally, can you provide screenshots of your settings?
When you say the game is running half of what it should be, it could be that you're simply expecting games that natively run at 30 FPS (Wind Waker, Skies of Arcadia, Twilight Princess) to run at 60 FPS. The best way to tell if a game is running fullspeed or not is to run Dolphin in Windowed Mode and look at the % Dolphin displays at the bottom. If it's running at 100%, that's the framerate you're supposed to be playing at. If it says 50%, then that's a problem. Make sure you don't have the VBeam Speed Hack enabled for any of your games (right-click game in Dolphin, then click Properties); the VBeam Speed Hack sometimes halves the FPS.
When you say the game is running half of what it should be, it could be that you're simply expecting games that natively run at 30 FPS (Wind Waker, Skies of Arcadia, Twilight Princess) to run at 60 FPS. The best way to tell if a game is running fullspeed or not is to run Dolphin in Windowed Mode and look at the % Dolphin displays at the bottom. If it's running at 100%, that's the framerate you're supposed to be playing at. If it says 50%, then that's a problem. Make sure you don't have the VBeam Speed Hack enabled for any of your games (right-click game in Dolphin, then click Properties); the VBeam Speed Hack sometimes halves the FPS.