I actually stuck a little plant in the top of it because I noticed that problem too.
Today Dory seems to appreciate the whole tank more and is hanging out in the front where I can see him, which is nice. His fin rot still looks real iffy, but I'm on the second day of the combo Maracyn medication so I'm not TOO worried (yet).
The parameters look good: Ammonia is at about 0.
One last question: How quickly is the cycle supposed to happen? I did add some gravel from his bowl which I assumed was cycled because I tested its week-old water before I moved him out of it and both the Ammonia and Nitrites were at 0 (I can't afford a Nitrate test yet, I have to get these things one at a time). If it was cycled, I assume that means it should speed up this process. I still don't have a good grasp of exactly how long it can take one small fish to foul up a 5-gallon tank.
Oh, and I attached some new pics too

Whitney