I just tested my Logitech Gamepad F310. First log-in it asked me to calibrate, so I did.
I then logged in with my character and configured everything to be gamepad friendly, and then I shut the game down.

I signed back in and it asked me to calibrate the controller again... so this seems to be the problem you're running into. However, I simply clicked "no" for calibration and continued to log in with my character.
Everything worked perfectly just the way I had set it up. I then shut the game down again and then signed back in. This time there was no calibration message.

That's how I fixed the issue, I've logged and relogged several times now without receiving the calibration message and my controller still works. I hope this can help you as well. =)