I think Brygun and whoever else mentioned dinos is probably on the right path. First thing you need to do is identify what exactly you have growing on the sand. There is a method that is easy to do to see if they are dinos or not.
This thread maybe helpful to you to find out if they are dinos.
If they are, follow through with how to eradicate them, some good info on this site for that. Raising P seems to combat dinos as with some elevated P levels, other organisms now can compete for that extra P and then outcompete the dinos and once they are eradicated, you can bring those levels back down but never let them bottom out!!!
If they arent dinos, adding sand sifters/movers and more flow is good. I keep a yellow watchman goby/pistol shrimp pair and boy do they move some sand. Also have (had) lots of nassarius (sp?) snails, a fighting conch and a sand sifting star fish. Lately, I've noticed the same stuff, dirty sand, but only in areas I know has lower flow due to rock and corals growing blocking flow. I upped that and it got better down in that one area. Lately, been noticing more and more. Sucked a bunch of it out yesterday. I think all my snails must have finally kicked it, Ive only seen maybe 1-2 at night lately. I have a valentini puffer that eats smaller snails so can only use larger ones but he still goes after them if they pop out of the sand while he's awake but generally they can get away if I tap on the glass and give him a stern talking to. LOL So, after work, Im off to purchase about 4-5 more (I have a 29gal). I still haven't rulled out dinos myself in my tank, so need to do that.
I keep seeing one guy (sorry man I forget your username) that pushes for a sandbed rip clean. This is something I used to do back in the day on my freshwater tanks as well as back in the mid 90s on my salt tank at home and at school in our marine bio class. 1-2 times a year, suck out all the sand/substrate, rinse really well till clean, and then stick it back in (salt tanks I just went to the beach behind the island to the back bay and got more sand). When I restarted reef keeping hobby back a few years ago, I read alot about not disturbing the sand. I always scratched my head on that. Then again, my tank is about 2.3 years old now and havent really touched the sandbed as the critters did a good job keeping it white and clean. But just yesterday during my monthly water change (yeah yeah, I dose) I contemplated doing a rip cleaning. Its alot of work and not really looking forward to that (I really dont have the time anyways) so Im going back the natural way with more sand sifting critters and hopefully I can score some worms as I dont think I have any in the tank.
Good luck!