Yellow water is caused by cleaning the screen without removing it from the system. No one does that anymore (at least no one who knows A from B when it comes to scrubbers). My tank is crystal clear.
Floyd is totally right on this one, yellow water among other issues have been solved back in 2008. Anyone who hasn't researched algae scrubbers in the last few years has very old and outdated information.
My tank has been setup since August 2010 (almost a year now) as an algae scrubber only system. Still running very well... Even better still I have the most ghetto built scrubber with low flow issues and lack of light issues, yet it still has no problems keeping up the tank. (I am getting ready to address the problems with my scrubber)
Algae scrubbers create an extremely forgiving system, I totally believe that if I had not had one in my tank. All of my beginner mistakes would have cost me a lot of money.
The most simple reason algae scrubbers are so effective is, algae is consuming nitrate and phosphate as it is made available. Therefore unlike traditional systems that need water changes to remove NO3 and PO4 and say a skimmer to remove un-eaten food, etc before they become NO3 and PO4... Algae scrubber systems can make NO3 and PO4 hit rock bottom "zero"... Algae scrubber systems don't stop there, so many benefits to running an algae scrubber...
Please do check out the Algae Scrubber Basics thread I started on RC (same username), it has been stuck in the "Advanced Topics" section
FYI my water is also crystal clear...