We took down old tile, scrapped glue, had to do a little patching of the cement board. We were told to prime it before installing the new tile. Well, the primer has had plenty of time to dry, but in the process of measuring for the centering of the new tile, the primer is peeling off. HELP! What did we do wrong????
I think you got some bad advice about painting the backerboard. I'm also a little concerned about your use of the word "glue." There should have been no glue on the surface of the backerboard.
At this point, I think it'd be best for you to remove the old backerboard and replace it with new material. Installing new tile is going to be expensive and time consuming. Treat yourself to a nice, reliable substrate to ensure that your time & money won't be wasted.