My guess is fraps shows the frame rate at the display. This is indeed the true fps which you see (without glasses). MSI Afterburner and EVGA Precision show "in-game" fps, which means fps generated by the game running on the cpu.
I am just trying to avoid confusion in the future. It's well known that v-sync is on when 3D vision is on. And I am 99% sure that v-sync stays on, even when 3D is toggled off via the emitter.
You wont see more than 120fps on a 120Hz monitor with 3D vision on. And that 120fps is actually 60fps from the game, which is doubled (left and right eye) by the gpu to make 120fps (as measured in fraps).