When I use my Cowboy Repeater+ (all mods) and crouched in VATS, I can no longer change weapon, aim, enter VATS or use my Pip-boy.
If I hold the right-button (to aim, although it doesn't aim) and then tap the left button, my character doesn't shoot, but the controls seem to be re-enabled.
Also, when switching to a different ammo type, even though I only have 6 of that ammo type, my character keeps reloading forever until I switch back to the standard ammo (which I have loads of).
This has only occured since the last compulsory patch from Steam.