After rereading your post, I might be able to contribute further.
I don't know about the freshwater monster fish world, but in the reef world bioballs are usually a bad thing. Since nitrates are so important to keep in check in reefs (nitrates are supposed to be less than 15, ideally 0 in reef tanks), a lot of reef enthusiasts put them down because they can actually increase nitrates due to gunk build up. To remedy this, they either completely remove the media or clean it weekly (with tank water). Also, do you utilize foam? Foam is another thing notorious in the reef realm for mysterious nitrate build ups. Try cleaning your foam, bioballs, and other media (again with tank water) and see what comes out. Make sure you clean with tank water as to not kill all your bacteria and result in a lot of headaches with a new cycle forming. You might also consider cleaning the bioballs/foam in segments (every other week or so) to make sure you don't wipe out your bacteria colonies.
Some people utilize fine-mesh foam in reef tanks to keep their tank water pristine clean. What they do is use a foam pad once a week, take it completely out of the tank and wait two weeks before returning it (air out). By doing so it eliminated all of the nitrate problems, but it also destroys the bacterial colonies. Since reef tanks generally utilize live rock for bio filtration, this is no biggie killing all those bacteria. But in a F/W tank this can be adverse, so you may consider using this method only if you have other bio filtration methods in addition to foams.
