How are you testing for bacteria? Wet slides, stains and a high-powered microscope? Because that is pretty much the only way to tell what you have or do not have living in your water. You can buy tests for ammonia, nitrate and nitrite, but there is no easy home test for bacteria.
The point of a filter in an aquatic biosystem is to remove solid waste, and even more importantly, to support and provide a medium for bacterial growth. I can guarantee that unless you are disinfecting that filter and changing the water every day (probably with sterile water) that you have bacteria in there (technically, you'd have them even then, just less). In no way do filters remove bacteria from the water, unless you also have a UV sterilizer and protein skimmer.
I mean, it looks cool and everything- just don't expect it to be bacteria-free. And it's going to be a lot of work to maintain it to the level that it will still provide rain-quality water.