If the water is contaminated with bio or viral organism, those filters may not do anything. But, if your getting water from an approved source, it may be nothing more than some contaminant that got in and found a nice spot to take up residence. Could be a crevice, on a seal, in some nook or cranny and no mater how many times you poke and brush, it's little offsprings are surviving.
The solution is regular toilet bowl cleaner with a disinfectant that's allowed to get into all the spots some microscopic left over bio-mutant-icky is lingering and kill it. There are also those RV black tank chemicals that also have a bowl cleaner built in, but you really want the stuff you use to stay around long enough to do the job. Just filling a bowl with cleaner and flushing it down doesn't ensure it's got into all the spots on it's way to the black tank.