Have you tested your water parameters in your tank - ie ammonia, nitrite and nitrate? Just because the others aren't reacting doesn't mean to say there isn't a problem.
if you don't have freshwater test kits, take a sample of tankwater to the petshop, it may cost a few dollars. Ask them to test and give you the results - get them to write the figures down for each one. Then whatever it is, do not buy anything the petshop advises to "fix" the tank. Basically, if ammonia or nitrite levels are over 0, you need to do frequent partial waterchanges (at least 20% daily on your tank).
It could very well be waste building up beneath the stones which could be causing a problem.