Now same issue when adding the F-14 module, so what I have done is,
open the new module input, go to axis, bind some settings, then exit the sim,
repair, restart the computer, restart the sim, go into the inputs and all should be working and rebind controls worked for me.
I think whats going on here, is everytime theres a new module of inputs added to the lua list, it goes haywire. so running this procedure worked for me.