I see a lot of people have looked at this, and nobody has replied.
I feel like I have the same problem in my 98tj, it's not that the heat is not working, it just seems to be slightly above temp. When you get into most cars, you have to turn the heat off, but maybe the soft top makes a huge difference.
I was thinking about it today when I was driving, because I remembered my heat working so well that I was commenting to people how amazingly warm it was. But maybe because that was in the fall, and not below freezing outside.