Ok folks, appreciate all the help.
What I did today.
Disconnected the battery and went through the whole initialization process again, and again, and again. Roof still won't close.
I had forgotten to mention one thing, not sure if it makes a difference but this has happened every time I have had done the initialization process. On the last step after the roof and shade have moved back together, the glass comes forward, but does not close. The shade has never closed.
Anyone know if this would make a difference. I do keep the close button depressed for a while after the glass closes and the shade does not close.