Computer Specs: P4 3.2ghz w/ HT, 7600GT 256mB, 2.5gB RAM, Audigy 4
Emulator Version: Build 727

I have tried messing with all the options and all my games play extremely fast, between 700-900% with vsync & triple buffering. Without those it plays around 1200%. It doesn't matter what game I play, it's always the same. This only happens with VBA-M, not VBA 1.8 Beta 3.

Disable speed->Turbo mode

If that does not help, move your ini to somewhere else and check if it's still too fast.

Problem had to do with my Input. When configuring my USB Controller, it set "Speed Up" to an invalid value (Input X-Axis). Correcting this fixes the speed issue.