How do I attack this problem

well thats odd, you bioload is very low to have a problem like this. whats your water change schedule like?

 

Every 2 weeks I do a water change 10 to 15 percent.

 

Are there many organisms in your refugium? besides chaeto?

 

Only copods and live rock.

 

ok i think this looks like cyano bacteria, there is one trick left to do.

there is a product called chemi-clean made by boyd industries, also another one called red slime remover.
you can use that it is a basic antibiotic(reef safe), that will disolve the cyano bacteria in your tank, while leaving other helpful bacteria alone. i think it says to turn off your skimmer and do 30% water change, i recommend a like a 30% water change 3 days in a row after treatment as it will release all the nutrients to in the algae. and 30% changes every week for the rest of the month. if you dont remove the nutrients after there released the cyano will just be replace by other types of algae.


another thing i would recommend is slowly removing your sand over a month or two(like a half a cup a day) until you get down to 1 inch. if you notice parameter spikes slow down and only do half a cup every 2 days.
as in my expierence very shallow sand beds are they only type to have in the main tank.

 

Are your corals and everything else healthy? If they are you probably don't need to mess with flow rates although moving the flow (powerhead) slightly nearer to the substrate may help. I would go with a herbivore to feed on the cyano and allow the DSB bacteria and chaeto to use up nutrients in the waste of the conch.

 

In my opinion I would definitely go with the biological method over chemical every time. There are always different options, not every option works for everyone.

 

+1 on above

my thoughts
I have been following this thread, the images do look like cyno
the sand bed you have is not deep enough to be a DSB and as such its just acting as a nutrient trap (have you tested Nitrate and Phosphates recently?)

this coupled with the area of low flow (which you do have based on your description of water movement and pump placements) means the nutrients in the sand are feeding the cyno

you may remove a lot when syphoning stirring etc but some is left behind and it rapidly regenerates due to the available nutrients and the ideal living conditions it has


Steve

 

Ive read that a DSB can be between 3 to 6 inches with a min of 3 inches. I agree with you that the deeper the better. I dont want to remove sand from my display setup, what are my other options?

 

IMO red slime removers are only a temporary fix, you need to fix the cause so I agree that a shallower sand bed in your main tank would help with more frequent water changes, increased flow rates, if this doesn't work then reducing your lighting by 1 hour may help. Phil