Rocks such as limestone can contain CaCO3 which can cause the Ph in the water to rise, CaCO3 is an alkali compound which acts as a neutralizer to the acid (vinegar), when an acid is poured on the rock the calcium carbonate neutralizes the acid therefore making it bubble.
It is never a good idea to boil rocks, they can contain pockets that can cause trapped air to expand and explode. Take the rock and scrub it real good (no soaps). Put it in a tub and full the tub with very hot water to kill off unwanted bacteria.
Always monitor your levels in your tank after introducing any thing new into the tank.