I posted with this same problem about 6 months or so ago in my 24g nano before it cracked. It drove me crazy. Same problem - low PH and brown "stuff" on the sand. Didn't act like cyno (wasn't slimy). I ended up reading something about tanks that are covered all the time (which mine was) and poor oxygen exchange, even with additional powerhead.
Could that be your issue? Is your tank covered? I uncovered my tank, did several good size water changed, and increased the size of my Koralia (and direction). The brown stuff on the sand looked more like diatoms. I even went up to 5 days without feeding. It did finally resolve itself. Also, lighting was an issue. It took me a while to realize that since the tank was in a classroom, I needed to take the fluorescent lights into account. Several years ago, they installed special fluor. bulbs to simulate "daylight" for the kids - sounds like prison huh! So, have you thought about oxygen exchange, lighting and water movement too?
These guys are wonderful. They'll help you think it through. I have learned a lot just by reading, reading, reading all their advice and posts. Your readings will be off if it is cyno or algae because it will consume phosphates and nitrates so don't go just by the numbers.