What do you have in the tank currently coral-wise?
I run my halides for 8 hours. The brown algae will go away when the tank finds its balance, there are a few stages of algae that can take up to a year to fully go through. First you'll have brown, and depending on the cleanliness of your source water (ex, if you don't use RO/DI, expect the brown to hang around a good bit longer as the phosphates in tap water feed it). Then you'll have green, not the long hairy stuff, but similar looking in coverage to the brown, but it may just stay on rocks, and not on the sand. Finally you'll have purple, coraline, the good stuff. I remember I couldn't wait to get some coraline going in my tank. Now it's just another weekly chore, lol.
Patience is a virtue, and a valuable habbit in this hobby.