Nailing direct stick?

G'day Guys, I'm in the middle (I wish, not even that far!) of laying a direct stick engineered floor over masonite (which in itself is over old T&G). I'm using RLA Polyurethane which is truly the work of the devil as far as I'm concerned, but certainly gives a nice floor to walk on. I had also been nailing on the joists, just using 1" cleats but about a metre into the floor I noticed my gun must be kicking up slightly and is damaging the edges of the boards.

I can of course investigate what's going on with the gun, but when I re-laid the first 2 rows ( that's another story!) I noticed the nails really didn't do too much when I lifted the boards. I'm wondering then whether it's even worth using the gun? It seems the potential for damage outweighs any real advantage and from my experience with that adhesive, that floor isn't going anywhere fast! The only caveat that I can think of is that the floor is not perfectly flat over a wide area, and perhaps the nails help hold it down while the glue goes off? Oh, I'm also running yellow cross-linked PVA glue into the top edge of the groove, then using a small paint brush to try to spread it a bit on the edge of the top hardwood layer. I understand that as well as bonding the boards, the PVA is designed to resist spills that may otherwise find their way through the joints.

Thanks for the advice.