I can understand how that might happen due to the porous nature of a matte finish versus gloss. It can trap flux and air. But it shouldn't be enough to cause any big problems. What kind of flux is it? Is it coming off cleanly when washing? To reduce the solder balls, you could try bumping up the preheat temperatures a little bit (~5 degrees) to increase the flux evaporation rate before it enters the reflow temperature zones. If there is too much flux when it gets to the liquidus temperatures, the gas pockets will burst and throw molten solder around. The other possibility is, if it is the same pcb, but sanded down to remove the gloss coating, it could be getting too hot too fast and that will cause the flux to violently boil off and splatter around. Again, you can adjust the preheat and/or ramp temperature ~5 degrees at a time until it stops.
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