Shadowcat: That's interesting. I don't use manual transmission, but I have noticed something similar when trying to navigate the in-game menus with the keyboard (arrow keys).
Does that seem like the same issue?
I think the menu navigation keys are fixed, but out of interest are you using the arrow keys for gear changes? If so, does the problem occur if you bind those commands to different keys?
Nope, I use the default keys for changing gears (S and A if I remember correctly). I use mouse in the menus, so I don't know if it's the same problem.