Hi cath,
Sand darkening (somewhat brownish?) is almost always linked to a
diatom bloom. If you scrape the top layer of sand off, you'll find lighter sand underneath (diatoms love light).
A tank can go through several (though weaker and weaker) pendulum swings before it settles down, and with each reset of the nutrient-vs.-bioload bob, diatoms are among the the first to show their numbers.
They're an exceedingly vital component of most marine systems, to be sure. And they rarely are unaccompanied by other 'darkening' organism populations (dinoflagellates, cyano, algae, etc.)
As for substrate profiles, that's a hot topic for some. I prefer to have area zones of all-rubble and large zones of all-sand (the latter is better for deep, live sandbeds for the sake of faunal migrations).
HTH