I just played with it a little. The back deck might be causing you issues. I made that 3 tiles deep, like the side decking, as opposed to 2. Normally, I would use a shed roof and on the corner, a hipped or half hipped, depending on the application, and blend them in to the same height.
But...a couple of patches ago, that started clipping in one area. I just, as I said, tried again to make it not clip and blend that clipped section, but it's almost like it leaves a hole, where the roof pieces meet. I saved it to my Library and I'll play a little more after dinner. I have to go cook, so my wife doesn't beat me again. :expressionless: