The rock could be leaching things that effect not only the pH, but alse be toxic to the bacteria. Or, the rock could be covering/smothering a good portion of the undergravel filter plate (if applicable). Or, the rock could have uneaten food or excessive poop trapped and rotting out of reach of the fish. Lots of variables.
Solution: Remove the rock, do water changes, monitor the readings. If you really like the rock and want to keep it, soak the rock/boil the rock. Not for hours, but for weeks. Maybe you can get it to the point where it is safe to put in the tank. Otherwise, you can seal the rock.