Actually, imo, your sump is arranged ideally for this purpose. Baffles are under-over then over-under, which is makes main flow take place at top part of middle section.
And I believe this is the best arrangement for denitrificating siporax. Oxygen and nitrate rich water passes from the top which makes a slow turbulence. This way, bottom part remains lesser oxygenated compared to top, allowing Anaerobic denitrification bacteria to establish, especially in the bottom-central parts of your siporax arrangement. Then, why they dont consume all the nitrates, because you are feeding the siporax section with oxygen-rich water, also (of course, not enough siporax can be another exp.).
I think, the best way to let denitrifying bacteria establish is allow them to consume the existing oxygen, and then start eating nitrates. And this requires to stop feeding oxygenated water for certain time intervals. My plan is placing eggcrate box in another glass box higher then sump water level and feeding it with a small pump, on timer. Frequent nitrite and nitrate tests may tell me when to flush the container containing siporax cage.
