My only experience with keybindings not working properly was caused by AGM having actions bound to the left ctrl key. Anything that used the left ctrl key would require 2 presses to activate (such as changing stances which would require me to hit ctrl+w or ctrl+s x2 for it to work).
I just went and checked my keybinds and found out that I have two things bound to my numbers on my numberpad. The default actions were from the base game and they were used to look around. TFAR adds keybinds that allow the numberpad to switch between the SW radios channels. Now when I use my numberpad I can't look around even though both are bound to the same key and both would be valid actions to be performed in the current situation. My guess is that some keybind is being overwritten somewhere by one of the mods. I'd try and give the radio controls unique keybinds from everything else and/or remove everything that uses the ctrl, p or ctrl+p key and see if that does anything. If it does, slowly add controls back to everything you removed until you find which one caused the problem.
Also interesting thing I noticed, some of my possible keybinds from the mods only show up when I go to edit them while in game. When I'm in the main menu I cannot access TFAR and cTab's keybinds while customizing controls. No idea what causes that but I get around it by just popping into the virtual arsenal and changing them there.
Hope this helps in some way.
