With a pH of 6.4 your beneficial bacteria is inhibited by 90% at a pH of 6.5. You need to get your pH to about 7+ to get it kick started so it can grow. Thoroughly cleaning you filter is washing off all the good bacteria. All that brown gunk is your bacteria going down the drain.
You don't want to thoroughly clean your filters, read here.
Sorry, no.Fishwonder are you the author of this guide?
Just curious, speaking of cleaning filters - I noticed after running the filter 3 months straight, it would not get the water clear. The water always seemed hazy. I then upgraded to a bigger filter for my 20 gallon, which cleared instantly, and now I figure, do we need to completely clean out the filter when the water cannot clear? I had replaced the cartridge too, at the time, and I do that every 5 -6 weeks.
Changing the cartridge made the water hazy. Unfortunately you bought a bigger filter for no reason.