Check the rinsing of the silane in IPA(quick rinse as not to rinse all of the silane off) and make sure that the excess silane is drained off before curing it in the oven. This is tricky to do, but it can be done.
There is probably too many Parylene flakes from other demasking operations in the air in your facility. Even a cheap clean room area will help to reduce this. Also, make sure the racks and monomer gas feed tube are cleaned on a regular basis. Small flakes can come off of the racks and land on the parts while they are on the turn table.
Regards,