Update: Ultra Low Phosphate
Many people, after having great success with their scrubbers, have brought their phosphate down so low that their test kits can't measure it. And the nuisance algae has been mostly cleared out of the display. However, these people start seeing a fuzzy detritus-looking accumulation on some parts of the rocks, and sometimes on the sand. They clean it off, but it comes right back. What is it?
What they are seeing is phosphate coming out of the rocks(!). This is a great thing to happen. It requires two situations: (1) You previously had high levels of phosphate in your water (higher than .1) for several weeks or more, and (2) You now have very low levels of phosphate in your water. It's very counter-intuitive, and it will make you think that things are going wrong, especially since this type of algae growth looks just like "detritus" (but it's not.) Things are actually going very right, and here is why:
Phosphate is like water: It flows from higher levels to lower levels. For example, if you have two aquariums connected with a pipe at the bottom, the water levels would be the same in each tank. But if you poured extra water into one tank, it's level would rise for a second, then the water would flow into the other aquarium until the levels were equal again (although both levels would now be higher). Now, if you removed some water from one of the aquariums, it's level would drop for a second, then the water from the other aquarium would flow into it until they both evened out again (although both levels would now be lower). If you kept removing water from just one of the aquariums, the levels of both aquariums would keep falling, until they both reached the bottom. This is exactly how phosphate works.
Situation (1): In the previous weeks or months, when your phosphate levels in your water were high, the phosphate was flowing from the water INTO the rocks and sand and anything else that is made up of calcium carbonate, such as coral skeletons and clam shells. The phosphate did this because it's level in the water was "higher" than the phosphate in the rocks and sand. This part of the process is invisible, since Inorganic Phosphate is invisible. You don't see it going into the rocks and sand, but your rocks and sand are indeed being "loaded up". And if your phosphate in your water goes up even higher (say, .5), then even more phosphate goes into your rocks and sand, until it evens out again. You probably also see nuisance algae on your glass and other non-rock surfaces, because there is enough phosphate in the WATER to feed the algae anyhwere it's at. And that's the important point to remember: There is enough phosphate in the WATER to feed the algae ANYWHERE.
Situation (2): Now, you've been running your scrubber (or any phosphate remover) for a while, and your phosphate in the WATER has been testing "zero" on your hobby test kit. Nuisance algae has been reduced or eliminated on your glass and everywhere else. This is because there is not enough phosphate in the WATER to feed the nuisance algae. However, since the phosphate in the water is now very low, guess where it's still high? IN THE ROCKS! So, phosphate starts flowing FROM the rocks and sand, back INTO the water. And as long as your scrubber keeps the phosphate low in the WATER, the phosphate will keep flowing out of the rocks until it is at the same level as the water. You can visualize the phosphate as heat coming off of a hot brick; you can't see it, but it's flowing out of the brick. Anyways, since you now have all this phosphate coming out of the rocks and sand, guess where algae starts to grow? ON THE ROCKS AND SAND!
There is a striking differece between the algae in Situation 1 and 2, however; in (1) the algae is on everything: Glass, rocks, sand, pipes, thermometers, pumps, etc., and the algae is a typical algae that you normally get in your display. But in (2), the algae is dark, short and fuzzy, just like detritus, and it's only growing on the rocks and sand. And if you look closely at the rocks, it only growing on certain PARTS of the rocks (usuallly narrow parts that stick out), and not growing on the rocks right next to it. This is because certain areas of the rock have absorbed more phosphate than others, and thus are releasing more phosphate into the water. Glass, plastic, etc, don't absorb phosphate, so thats' why there is no algae growing on them now, since they are not releasing phosphate back into the water. So the algae now grows only where it can find enough phosphate, and for now, this is only on certain parts of the rock and sand where enough phosphate is flowing back into the water.
But just like the aquarium example above, the levels of phosphate in the rocks and water will eventually even out, and the flowing will stop. When this happens, the nuisance algae will disappear from the rocks, never to return again (unless of course your phosphate levels rise again for some reason.) The time for this to happen is weeks to months, depending upon how much phosphate is stored in the rocks. So don't give up!