I'll start off by saying I have read almost every online forum about brown algae in new tank setups. As much as I read, I can't imagine my tank being normal. First is my setup. I have pressurized co2 which I've calibrated to as much as I can pump in before fish gasp for air, Normal dosage of Seachem Flourish Ferts(2 caps/week) and 4 54W T5HO bulbs on 12 hours a day. I used to keep the lights on 8 hours a day but with 12 hours I have boosted plant growth and pearling. After switching to 12 hour days, the brown algae took over the plants in the tank. I currently have my tank blacked out for going on day 2 now to attempt to kill it off. Will I never be able to keep my lights on 12 hours without the resulting algae?

Then you should know it's most likely a diatom issue and will go away on its own in time.

Will it damage or kill off my plants?

no, just keep up with your water changes and whats your light time frame?

Rub it off the plants and surfaces first, then do a small partial water change (25%), repeat every 2 or 3 days until the tank cycles and the diatoms go away on their own. Get you some otocinclus cat fish, they do real well on cleaning up diatoms. Mine cleaned the plant leaves better than I could rubbing the stuff off with my fingers.

Ive had 5 Oto's in my tank for about two weeks. Right now I have no light on the tank. It started getting worse when I went to 12 hours a day. I guess I'll cut it down to 8 hours when the diatoms clear up.

Partially true, diatoms don't always go away on their own. If your water source has a lot of silicates you may always have a diatom problem, its not a guarantee but its possible. Example: My tap water has 8-15ppm silicates in it, if I use my tap water in a low light tank I get diatoms. Now if its a new tank and your water source has really low or zero silicates then yes eventually they will go away.

Yea greaser because I don't have that issue I don't think about that condition.