Gunner special interferes with Grenades and other specialties !! whassup ?:
So the Gunner, as a Specialization, is necessarily going to lock out usage of the other Specializations. You can only have one equipped at a time.
That means the Minigun will become your active special weapon and the Gunner Spec tree will become your active skill tree.
If you're running into issues with the grenades, make sure you swap onto the proper grenade - or swag onto the standard grenade before changing Specs.
Let me know if there's still any questions or confusion.