I do not have this mod, so I am unable to duplicate your anomaly, but my guess is that the shifter position in the ".car" file is defined incorrectly. It is a bit tedious but you can edit the position yourself if you are willing to keep tweaking the coordinates until you get it right. Open the ".car" file in a text editor look for the following line:
ShiftStickPosition=(<x.xxx, xxx, x.xxx>)
These coordinates usually adjust as (+ =Left / - =Right), (- =Down/+ =Up), (- =Forward/+ =Backward) but there are exceptions.
I could possibly be of more assistance if I knew exactly which mod you are using.
Good luck!