re:Weird smell - Have you tried isolating a small bit of of the bacteria on some clean media for a day or two apart from the housing and the rest? It would be interesting to also isolate a second piece with the bacteria treated on media that has been exposed to ammonia/waste, but now separate from the system.
At least you'd have a better indication of whether the smell is the bacteria itself (over time/exposed to air), the bacteria reacting to the waste/ammonia, or possibly as kevin mentioned - you're off gassing carbon.
hehe I love doing experiments.
kdh, I'm curious, have you ever tested your pond for iron? I have no idea how much might be in lava rock, if it's pure or an alloy, etc. nor if there is any danger of it being released when immersed in pond water over a prolonged period of time, or exposed to ammonia and other pond chemicals. I just got to wondering about this now because I'm currently making a list of heavy metals to test for in my well water that are toxic to Koi (iron is one of them!) so the mention of iron in the lava rock got me thinking.
I didn't know that lava rock was getting a bum rap.
I thought a lot of folk were still using it in their trickle tower filters, etc.