Ive been following a thread of RC and what you describing about it dissappearing at night leads me to think it maybe dinoflagellates as per the info on that thread as they take to the water column at night and settle during the day.
It may very well be new tank syndrome.
There has been a few theories. Blackouts, Uv, dirty method. Dosing of phyto and bacteria etc.
Hope you get lucky eradicating it. Thers some success stories so dont lose hope