Ok guess what happened? After I loaded the game and played a family then moved them out of the lot and onto another lot the high roof returned. I since have put it down to a few possibilities:
1. The flatten lot tool. After I have used it I get the high roof.
2. I had WitchyWoman's Invisible Driveway installed but I haven't used it. I deleted it and low and behold the high roof had been corrected when I replaced the roof.
3. My game doesn't like the invisible driveways or
4. Freetime is doing this problem. I never had the high until I installed freetime.
5. A combination of all those things.
Uninstall is out of the question it takes too long. I am going to apply for holidays in september october then I will do an reinstall. I hope they will release a patch and see if that will help my problem.

See in that pic the green square? Well that is where I can place the level tool. Maybe that is part of the problem.