Some people are surprised when their nitrate goes to zero, but their phosphate only drops to a certain level, and stays there. Could it be that their scrubber "nitrate limited"?
No. What is happening is that the rocks (and maybe the sand) are releasing phosphate back into the water, slowly. Rocks, and to a lesser extent sand, absorb phosphate like a sponge. When the scrubber removes phosphate from the water, the rocks put this phosphate back into the water. This can last for weeks to months, depending on how much phosphate was in the rocks, and how fast your scrubber is removing phosphate.
At first, the phosphate coming out of the rocks can cause additional algae to grow on the rocks, but this will fade away after weeks or months. However, even when it fades away, phosphate is still coming out of the rocks. It has to, until the phosphate "inside" the rocks equals "zero", which is what the phosphate in the water is trying to reach too.
The stronger your scrubber is, the faster this "zero" situation will happen. Also, the stronger your scrubber is, and the more flow-through it has, the more likely you will measure "zero" phosphate in the water even though some phosphate is still coming out of the rocks. This is because as soon as a little bit of phosphate comes out of the rocks and goes into the water, it is pushed into your scrubber and absorbed by the algae there before it can ever build up enough in the water to be measured. If your scrubber is weak, however, even a little phosphate coming out of the rocks will build up enough in the water to be measured.
Ironically, the phosphate that you measure in your water can actually increase after the nuisance algae on the rocks goes away. Why? Because that nuisance algae was consuming the phosphate as it was coming out of the rocks; with no more algae on the rocks, the phosphate that comes out of the rocks just goes into the water, where it will be measured by your tests unless it gets sucked up immediately by your scrubber.
Also, even more ironically, the more and faster your scrubber pulls phosphate out of the rocks, that more this phosphate will "hit" any corals that are on the rocks. And it will occur most at the bottom of the corals, where they are attached (and are nearest) to the rocks.
So the normal progression of a tank with bad algae problems might be:
1. Bad nuisance algae everywhere (water may test "zero" for nitrate and phosphate because the algae consumes it.)
2. Add scrubber.
3. Nuisance algae goes away from bare plastic, glass and sand, but increases on rocks. Nutrients in water may go up, or down.
4. Corals may turn brown where they are attached to the rocks.
5. Nitrate in water finally goes to "zero", but phosphate only drops to a certain level.
6. Nuisance algae on rocks finally goes away. Phosphate in water may go up.
7. Finally, all phosphate is removed; water tests "zero", and no more nuisance algae is in tank.