It is apparent that you have a contaminant which is rising to the surface of
the LPI after curing. This is verified by the fact that when you clean with
alcohol it improves. My suggestion to you is to have an FT-IR run on the
surface and see if you can determine traces of silcone or a plasticizer which
will give a similar affect of de-wetting. One possible solution is to flame
treat the boards prior to putting the conformal coat on. This will burn off
the surface contaminant and allow the coating to adhere. As far as long term
effects, there are no answers.
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