Hmm, in theory, I'd say you'd be correct. If the signal is being modified, I'd say the stock gauge would read less than normal, but I seam to remember mine still going straight to the top, and I was using the same "black box" FCD. I later got rid of it and just plugged the hose, thus eliminating fuel cut all together. Now, my stock gauge doesn't function at all.
I'd say hook up an aftermarket gauge, just to be sure. The stock one is pretty useless anyways. And if you're going to up the boost (which is why, I assume, you put in a FCD), you'll need one anyways.
If your car seems to be running normal, I wouldn't worry too much about it. But you're gonna have to up the boost to test your FCD anyways.
Good luck, and have fun!