You could try washing before priming to remove any contaminates. Use a strong cleanser like trisodium phosphate (TSP). Something else to try is another type of primer. Oil based primers, like Kilz, do a good job and can stick to questionable surfaces.
Fixing the Bubbles
Scrape off the bubbles and spot prime the area(s) with a oil based or tinted shellac primer. The areas can be spackled, sanded smooth and spot primed before touching up with your existing paint.