Nail Gun - Finish Nails Video

Help! Using finish nail gun and want nails flush, don't have time to caulk a million little holes before staining. The stain covers nail heads just fine as they are very small. The problem is trying to get the nail gun to flush nails, I have it set on flush and have practiced on scrap but, variations in the wood cause it to either indent or not set all the way flush. The result is a lot of countersinking I have to caulk, some I have to punch on in, some shoot flush and are ok but you don't get uniform consistent flush nails. Nail gun and air-compressor are new, seems to be working properly, is this just the way finish nail guns are. Any tips or help would be appreciated. Lots of stained trim to do. thanks!