whoever coined the term "nitrate factory" the first time must have had a screwy test kit, because the increase really isn't all that dramatic from my own experience. losing the bioballs in my system dropped nitrate from 5 ppm to 0, which really at that level is not a big deal, and this was in conjunction with a fuge, which also mitigated some of the trates.
new research is also showing that smaller ammounts of nitrate in your system may be requisite for proper coral health and growth, so striving for nitrate free systems could soon become antiquated. borneman hints on this in his book, as well as occasionally in his message board on another site.
if you run bioballs, and do not want them to become a problem, just clean some of them on a set schedual. if you do 25% of them a month rinsed under your water change water to remove sediment you will be more than fine. it is people who let their bioballs sit unattended for 3 years that are creating "factories" (and not just of nitrate) which actually is saying more about the lack of care that these people take with their system than the filtration method its self.
any residual nitrate that you have if you keep them clean will in most cases be kept in check by a healthy refugium. i would still be running my balls today, but my old fuge broke, so i had to use half of my sump for macro algae, which necessitated ball removal.
there are a couple other sites that you can go to with forums full of actual test results and advice by researchers and professional aquarists if you are interested in getting more fact than folk lore. can't post the link here, but if you email me at
krux@lanset.com i can forward it to you. just be sure you are looking for hobbyist advice when you ask questions, and that you are not looking for expert advice, unless you find a forum for your question that is frequented by actual experts. i have made a habbit of checking multiple communities whenever i have a question, as a bandwagon syndrome can hit places from time to time (it happens everywhere).
if you are about to start a new fuge, i would suggest that instead of going with grape, you instead look for a non caulerpa species, like halimeda (if you arent worried about calcium levels) or spaghetti algae. neither of these go sexual, a caulerpa tendency which occasionally strikes, releasing all of the nutrients that it has taken up back into the water, fouling your water both chemically and visually. of the caulerpas, grape is one of the safer ones though, so if you like the look of it, just be sure to always remove the oldest stuff first. bang guy probably has more algae tips if you are looking for more information.
oh and keep looking, you will find other peoples posts which will disprove my own findings point for point i am sure. thats one of the great things about this huge science experiment we are all working on together while we learn from each other.
hope that helped, and good luck.