This sound like a phenomenon that we used to call "blushing" Testing showed
that moisture (good old H2O) was seeping into the coating and bonding with
some of the fillers in the coating that have a lot of sites in their
molecules for hydrogen bonds (water loves these!). The end result was the
white haze or "blush". This is a totally reversible situation and can be
eliminated by baking the board for about 20 minutes at 250 deg F (you drive
out the moisture and away goes the blush).

You may want to consider giving your assembled boards a drying step (say 20
minutes at 250 deg F) before you apply the conformal coating because the
moisture may be coming from the inside, not the outside. Its worth a try!

Hope this helps.

Larry Fisher

Allen Woods & Associates