It is very important to know the cure conditions of both coatings,
application procedure and thickness. One situation you want to avoid is
overcuring the solder mask prior to conformal coating application.  It is
true if you apply a thicker coating you may solve the problem, but that is
neither the right approach or the best approach.  Your system could be clean
but totally overcured where anything you apply may have adhesion problems.  
There are other possibilities, but first provide the information above.

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