I would agree that, from your photos, it looks like dinoflagellates.
Last year, I struggled with dinoflagellates for months in my stony coral propagation system. I assumed that the treatment was the same as for any other algae or cyanobacteria; however, nutrient control, (extensive) manual removal, and turning off the lights for a few days didn't seem to make even the slightest dent. They kept coming back, would literally grow on anything and everything, and would spread like wildfire (after just removing a patch of them, they would completely grow back in only a few hours).
Finally, I decided to actually do a bit of reading on the subject, and I stumbled upon this helpful article from Randy Holmes-Farley:
http://reefkeeping.com/issues/2006-11/rhf/index.php
I set up a kalkwasser drip to keep the pH constantly elevated to 8.5 - as Randy outlines in this part of the article:
http://reefkeeping.com/issues/2006-11/rhf/index.php#12
I went home for the weekend, and when I got back to the lab that Monday, the dinoflagellates were completely gone. Needless to say, I was shocked - expecting the treatment to take a week or more before I saw any results. I didn't see any sign of them after that, and I haven't seen them since.