In your video options, there should be a vsync option (also may be called 'lick to refresh rate). Try unticking or ticking that (depending on how it is currently set). If it is not present, open the cfg or ini file in notepad and look for vsync. Set it to 1 or 0 depending upon the current setting.
Also, if you have a video card, go into the control panel for that (Catalyst Control Centre for AMD cards, NVIDIA control panel for NVIDIA cards (duh!)) and ensure vysnc is disabled there and not forcing an application override of vsync. Then try again and report back. It's an odd problem you have here.
You could try a different emulator, like the aforementioned Gens... If I run an emulator and it behaves in a manner I do not expect, I switch to something else.