I too have had my D100 since September and yes, I had the firmware 2.0 upgrade - which had nothing to do with exposure issues - just technical issues involving Adobe, fast compact flash cards, etc. I chuckle when I hear people talk about night and day differences in exposures after the V2.0 upgrade - kind of like the placebo effect. Again, if you go to the Nikon website, the upgrade information for the D100 will tell you specifically that it addressed purely technical issues.
I, along with others on various forums - to include Nikonians - have indicated our concern that there seems to be a great camera-to-camera reliability problem among the D100's. Prior to shooting with the D100 I was using the F5 and F100 - which I still own, but I was not prepared for the underexposure scenarios that I experienced with my D100 . Yet you will read where some love the exposures - "right on" they say, and that's great. But you will also notice a sizeable number of forum visitors who complain of the overall underexposure issue, only to be often ridiculed by other Nikon D100 owners who balk at anything that detracts from that model or Nikon in general.
I am definitely NOT satisfied with this D100 underexposure scenario, but I have seen the photographs that the D100 is capable of taking and let me tell you, they are awesome. Since then I've been experimenting with custom tone curves - which you need Nikon Capture for - and they have helped somewhat.
The big thing is learning as much as you can about exposure. Remember, there seems to be a trend whereby many photographers assume that jumping into digital means forgetting about photographic principles in general. With that in mind, I've learned NOT to trust my camera meters. I use an incident light meter - the Gossen Starlite - and I also use modified forms of spot metering. I only use Matrix when I'm assured I have a scene with predominantly neutral colors - and even then I rely on the custom tone curves.
But my biggest surprise - a delightful one at that - was when I also purchased a Fuji S2 Pro a few months later. Believe me, I am an avid Nikonian - to use that term - but I've got to tell you, that I now reach for my Fuji more often than not. As I said in other threads, I don't look at the S2 Pro as a Fuji, but rather as another Nikon product that Fuji just happened to tinker with! But if I didn't have the S2 Pro, I would be using my D100 just as much as I could, learning it's shortcomings and overcoming them with knowledge, procedure, and help from other sources - external meters, recommendations, etc.
Because I have both cameras and have used them enough to know, I can honestly say - in my personal opinion - that the Fuji S2 Pro blows the D100 out of the water with out of the camera color and exposure balance and saturation, and the flash scenario is even better. I get between 500 - 600 photographs with the S2 Pro before recharging or replacing batteries. But again, I love the D100 also, but in my opinion - and others also - the camera-to-camera reliability issue has left me wondering why Nikon couldn't improve upon this model better than it did.
So don't feel bad. By all means get your camera checked out, but my guess is that nothing will change. At that point you can learn to experiment with custom tone curves - which work in over 50% of scenarios - or, well...if you have the bucks, sell your gear, and perhaps purchase something else. Remember, I believe they call that a free enterprise system - that is, if you are unhappy with something after testing it out enough, you can opt for something else, provided you have the bucks to do so. I've had to stop buying anymore big stuff because I ran out of family members to sell.