Are you giving the flash enough time to fully recycle? If you fire to quickly before the flash has time to fully recycle then you will get some underexposed images. The strobes for the background may be set at full power while the flash on the model may be set at 1/2 or 1/4 power. If so it will take the strobes on the background longer to recycle than the strobe on the model. The models strobe may have recycled but the strobe on the background would not have hence the background underexposure.
If your shooting strobes in manual mode, where you have set the aperature to f8 per your light meter and if you have also set the cameras shutter speed to the 1/125th or longer for the D100, the fact that you have the in camera meter set to Spot should not make a bit of difference, just like in a camera with Film. Unconciously it may be that when you set to Matrix you were more comsistent in the timming between shots and allowing the strobes to fully recycle.
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