That is strange. Have you tried NOT nestling to gunsight? Can you shoot accurately using the floating ring? I noticed that Ricky uses that mode occasionally also, and I tried it, and had success also (mainly advantageous as a Central gunner). However, that mode does make it easier to hit parts of your own plane, since your gun is shooting from significantly below your direct line of sight.
At one point, I tried to alter my "home" (numpad 5) view for gunners; although it was centered properly, I wanted it to start out at or default to a fully zoomed out (widest FOV). The normal view is somewhat zoomed in when you first take control, and I don't like that, especially if I'm in a hurry to see an inbound attacker. In any case, it seemed like it was working at first, but later it just worked as if I had done nothing to it. So for me, it seems as if I can't change the home view for the gunner by saving a new one.
In trying that, I noticed something that I never really thought about too much: when nestled to gunsight, you can move your head around independently from how the gun is slewed. If NOT nestled, your view is controlled by the mouse, when moving the gun only; you can't move your head separately.
Like Ricky, I also have the "home" numpad 5 view mapped to my gunner control 4-way hat on my stick; but my need for it has been mainly to get the gun normalized when it get's "lost" (jammed fully in one direction trying to get to where you're looking when you take control, like a stupid robot butting his head against a wall and getting stuck there). It brings the gun back to where you're looking, but I've never had the misalignment problem ever.
Can you make a video of the problem? Maybe we'll get some inspiration as to exactly what has changed or happened.
One quick thought that screwed with me recently....if you're trying to get something to work that's controlled by the numpad and it won't work, make sure the Num Lock is on (easy to turn off accidentally when hitting 7 or other numbers near it when in a hurry). If you reboot, it should start with it on, but if it doesn't, you might have to figure out why the keyboard state on boot up has changed.