Flash compensation not working?

I'm using a Nikon D100 and the pop up flash (yes I'm aware I should get a separate flash for the hot shoe) and my camera is on manual. When I change the flash from +1.0 to --3.0 using the flash compensation button (indicated by the lightning sign and +/- ) there's no difference in the lighting of the photo or the strength of the flash. Any suggestions?

You may be too close to your subject. I used to have two Nikon D100 cameras and the flash compensation button worked just fine.

I used the on-board flash to trigger a couple of SB-600 flash units usually set to -2.0 before I could afford some real studio flash units. The out put was strong enough to trigger the SB-600's and add some specular highlights in the subjects eyes, but not add a noticeable amount of light to the scene

I set the lighting ratio using a Sekonic L-308S with the flash units set to be slaves in the manual mode. If I needed to reduce the light output of one of the flash units, I just dialed down the output on the flash and took additional readings.

Set flash compensation to zero and raise f/number instead.