Had something similar on a bike panel I was painting, what ever I did it would react and also couldn't work out what was reacting with what. I flatted it back and then used an isolator then carried on. It worked and got the job done but never did work out why it reacted in the first place.

Just out of interest, your first shot shows the clear over base but the other show something lighter. Are these your primer stages showing the same reaction all throughout the pain job?