If I understand correctly, you have a 120 Hertz monitor and because the FPS is below 120 and fluctuates, you think there is a problem. The FPS adapts to the Hertz number through VSYNC. This can also be switched off:
vblank_mode=0 glxgears -info
If your monitor is operating at 119.95Hz, then the monitor is doing this constantly. The FPS does not say anything about this.
Probably related? The CPU governor influence the refresh rate.