Project Sand Cleanup

I moved a rock a few days ago that has been a base of my rock structure for a long time, and I was surprised to see the disgusting brown cloud that erupted from under the rock, clouding my tank for hours. Since then I have been doing water change after water change vacuuming the sand. Could such polluted sand be what is holding the nutrients fueling the cyano in my tank? Also, what's the best way to clean sand? I have a gravel vac, but it was taking too much sand up so I put some netting over the mouth. This works pretty well, but the sand clogs it up and I end up having to restart it a couple times.

 

Is it better to just leave it alone?