You could be shoving the 9mm down in anticipation of the recoil. This doesn't have to be a flinch, Jeff Cooper calls it a Pre Ignition Push (or something like that). He has seen excellent shooters push pistols down when the hammer falls on a dud round, or an empty chamber. Since they shot very well when the gun was loaded he theorized that, when shooting fast, they were pushing the gun to control recoil and move to the next target FAST.
One theory, but it might not be the right one. How you place a handgun on a rest can sometimes also affect the point of impact. I've had some autoloaders shoot to different places when I rested the butt on something, than when I rested my hand on it.
You might be flinching because the 9mm has more recoil and is louder. Try having someone else load the gun, sometimes leaving the chamber empty, and see if you jerk or flinch when the hammer drops. The recoil of a shot can mask this.
HTH.
