Graham Naisbitt is definitely an expert on conformal coating, he has posted answers here for years.
Check your material to see what the cure mechanism is. Most urethanes need moisture from the air to cure, the higher the relative humidity the faster the cure. If the coating forms a skin before all of the solvent has had a chance to escape the solvent will form bubbles inside the coating. A little less humidity and you will end up with a matte finish, if it is really dry you'll have a slow cure that could be a shiny surface. If this is the problem, any areas that have a thicker coating would be the most likely to show bubbles.
Another possibility is the coating material is reacting in some way with the potting material. To check this out you will need to find out what the potting material is and then talk to the coating manufacturer. It may mean you have to change to a different brand of urethane.
Good luck, Mike F
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