I was thinking it might be that. I was firing the cannon at the entire hull rather than specific modules. Thanks. I used to sub target the power plant but then read that it doesn't take damage off the hull and as the hull always seems to go down faster (probably because I keep missing the module) I stopped subtargetting. I think I will start subtargetting again.
I swear by subtargetting. Get close, get above/below, use your thrusters to hold position and jackhammer the power plant. Vulture and FAS were made for this, cant comment on the FDL but I will whats what when I get one