Repaired the roof, replaced the bubble dome...

That's very very odd, I'm going to guess it was likely the material the original dome was made from. I just put in a brand new dome on top of the raised roof I added over the bathroom as part of my Amerigo remodel, and it stuck down to the lip with gusto (this may be working because I didn't put any caulk down beforehand as the dome ends flush with the edge of the raised ceiling sides).