I suspect that the problems you;re having are somehow related to the introduction of the mouse control for flying. First, of course, make sure that your controls are set to joystick and not mouse control (I think they've set the default to mouse control for the noobs).
Assuming that you have the joystick setting checked, you'll still need to check all your camera/view settings to make sure something didn't get set weird during the update. If you exported/saved a copy of your old pre-patch settings (as you always should do), try importing/loading your old settings back in (be sure to hit the "apply" button after doing so), and see if that doesn't fix your problem.
If not, you'll probably just have to go through every setting that has anything to do with camera/view and make sure that (i) they are set like you want them, and (ii) there aren't any conflicting, multiple assignments that might be causing some problems.
I'm not sure if it's related in any way, but my TIR has really been acting up since the last update as well (in both RoF and BoS), so I don't know if my TIR is has just gone on the fritz or if they made some similar change to both games that has gone screwy somehow. It's probably just my TIR, since if it were the games we'd probably be seeing more posts about problems like this, but it does make me wonder sometimes.
[EDIT] - turns out the TIR problem was on my end as suspected - I just unplugged the USB cable for the TIR and re-plugged it, and everything is working fine again. So, apparently not related to whatever you're seeing - I think it's most likely to be one of the controls settings things mentioned above.