Is it possible you are hitting the "auto-sprint" key? Mine is set to right shift.
If you have it on I am unable to shoot a gun and unable to crouch/prone with nothing equipped which is what it sounds like you are having trouble with. Check to see what your auto sprint key is assigned to and re-assign or just be aware of it and you cant hit the sprint key (left shift for me) briefly to turn it off and will allow you to shoot etc..