OK thanks for the new pics. My best guess is that you have a couple things going on. I think the brown stringy/goopy stuff looks like dinos. Although, I don't see any air bubbles trapped in the goop AND dinos are light hogs so they're usually found high up in the tank (unless you have pretty good PAR at your sand level). Those two caveats are preventing me from saying dinos for sure. The other thing going is that green/brown stuff on the sand. That kind of looks like diatoms, but it could be other things.
Can you let us know what your parameters are? Temp, salinity, pH, Alk, PO4, NO3, and (less important here) Ca and Mg? Also, what are you using for lights and what intensity/program are you running? Other tank details (size, major equipment, etc.) would also be helpful.