Does the algae seem very light and whisp-like? If so, then you almost certaintly have brown diatoms.
I had the same problem bigtime when I setup my 10gal. Believe it or not, some 3% (food grade) H2O2 really did do the trick. What it does is oxidize the algae, turning it from brown to a green or even whitish color. It is then significantly easier to remove and did not come back readily, at least for me. I treated the tank while it had HC and DHG in it, and neither plant suffered unduly (though most of the HC was beyond saving at this point).
DISCLAIMER: I did not have any fauna in the tank at the time. I do not know about whether or not this will have any longterm effects on the tank. I simply had tons of brown diatoms, and it was either dose the tank with H2O2 or scrap all of the plants. I was very satisfied with the results. Your mileage may vary.