They are not the end of the world, just a big ol PITA. Lots of time, lots of reading on how to get rid of them. I think it has to do with an imbalance in nutrients, but I don't know for sure.
I have one of my tanks that was pretty much empty ( shrooms and softies, thats it) that I've pretty much neglected for who knows how long. Dinos pretty much took over the tank. No algae, just dinos. Wish I had taken pics. When I decided to start playing around to see if I could get rid of them, NO3 was 25-40 and PO4 was low, .03 on a good day. I haven't done any of the conventional recommendations yet- blackout, raise ph, etc. Since I currently don't need the tank, I figured I'd mess around and see if there was anything else that would work. I started dosing phosphate, enough to raise the PO4 about .5 ppm each dose. And a little carbon- 2ml of vodka a day. Been doing it for a couple of weeks now. Nitrates are still stuck about the same, maybe a little less. But the dinos are turning from that snot-green-brown to a dark brown and slowly disappearing, and what is left is no longer producing air bubbles. As a plus, seems the softies are happy to have some food in the water column. Whether its the carbon or the phosphates, I don't know. But they are definitely happier.
Whether this will completely clear them up, I don't know. Thinking I'll try adding some Special Blend if things start to slow down. Definitely not the fastest way to get rid of them, but if I learn something along the way, it'll be worth it.