just a question was one a matt paint and the other a satin or gloss?
that mix sounds to me one of a few things one being that one paint was a matt mixed with a gloss or similar, the other could have been your air gun how far away did you spray? if you sprayed to far away the paint may have been drying just as it hit the hull this is a common problem with all spraying of any form, the other is to close you could have pushed to much air over the hull leaving bubbles, or runs which are more common in spraying to close and finally dirt on the hull before spraying did you wipe down the boat first?
What are you spraying onto wood or grp or abs? if its wood you should use a decent wood sealer before final painting, filler on low points etc, grp make sure the surface is dead smooth, same for abs. before you spray be sure to wipe down the area with some sort of cloth that will remove dirt and grit of the surface ( i used car body work wipes) did you spray a primer as a base coat?
heres my method for a nice finish ..
sand hull up to 2400 grit wet and dry, wipe down spray primer check for high and low spots fill with car body filler, and sand, sand low spots, primer again re-check for anything missed , i tend to do between 2 and 3 coats of primer on the hull ( thin coats! ) light sand with 1200 grit and wipe down, spray base colour ( 2 coats generally ) then mark water line sand 1200 up to or above waterline pending on base colour wipe down and mask and spray water line, 2 coats again generally wit till dry and sand whole hull lightly with 2400 and then clear coat 3 light coats generally with a light sanding with 2400 inbetween. once fully dry i give it normally a week ( allthough 48 hours is fine) then i buff it out to a glass finish
i can use this method for both air brushing or spray cans