[ejwsr]

First, did your HOB fuge/algae filter have an independent light source? You need a light for an energy source for photosynthesis to occur.

Flow rate. I would think that it is too high. A 46 gal tank should have a skimmer that processes 10% capacity per hour or 5 gph. The longer that the water is in contact with the air bubbles in a skimmer, the better adhesion to the bubble and the dryer the foam output.

Flow rate part two - Here is where there can be a great deal of debate, but it boils down to attaining two mutually exclusive goals:
High current in the tank
Low flow rate thru the filtration system.

High flow rates are good in the tank because it will keep detritus suspended until it hits your filtration system, keep corals and fish happy and healthy and there is an aesthetic value to seeing everything swaying in the currents.

Low flow thru the filter is critical for a few reasons:
In a natural system the nutrients can't accumulate because of the massive water movement. What nutrients are there are absorbed slowly by the algae and bacterial colonies. And slowly is the key for the closed tank environment.
Cellular respiration/metabolism is a slow process. The nutrients have to not only make contact with the cell, but in most case need to be passively transport across the cell membrane. Think about how an RO unit works and the picture becomes clearer. It takes time, osmotic pressure, etc just to get to the metabolic mechanism of the cell. The conversion from nitrate to N2, O2 , carbohydrate or protein synthesis also takes some time. It has been a long time since I studied molecular biology, but I do remember at least 6 steps or elements that have to happen.

You have to give it time to do it's thing, hence the low flow through the filter. Or at least through the algae refugium part of your filtration system.