My first thought is why are there these blobs of dicor in areas where there are no, seams, antennas or vents. Second thought some things going on under the roof material? You said "From what I read when a rubber roof swells it's because it was attacked by solvent", did you use a lot of alcohol that caused this? I have fixed a roof before but never saw this. Too many questions best one is it under warranty if yes take it in and let them look.
Think about things before you do them make life easier not harder.