Caddy:
The almost exact same thing happened to me when I had the TOR and Tune installed a few weeks ago. In my case, I brought the bike in with a complete full tank of gas. Immediately after the work was done I noticed that my fuel gauge had 0 bars... (but the tank was still full)
Both the mechanic and I were confused so he told me to first take the bike out to make sure I was happy with the exhaust while he would investigate how the gauge could have gotten screwed up during the download. After about 20 minutes of riding the bike (luv that new TOR sound

), the gauge started to creep up back to full. By the time I reached the dealer, the gas gauge was fine.
You might want to take a spin for 15-20 minutes and see what happens...perhaps the bikes brain needs some time to readjust itself to it's new config....