It's definately not wool daubers. Cause wool daubers cause "streak" like applications, and are harder to "even out". Dauber application isn't as even as dunking or airbrushing. The sealers wouldn't cause those marks. Sealers act like clear coat paint.Some are really shiney and some are less. Resolene is a less shiny sealer than supersheen. They dont really darken things unless you have lacquer in it. Or some kind of coloring producer. Like, if you had darkening neatsfoot oil conditioner then yeh, it could do that. But, it wouldn't make sense to condition just a "part" of a square. It looks like "over-dyeing" residue, settling to the bottom of the square. Then they just sealed it all. Oh, and it might be a double dunk. (dunk, dry, dunk) When you take it out the first time, the dye seems to spread to the outter most edges first if it's layed flat on the rough side. So, if you tilt it up and let the dye run all the way to the bottom, that might be the right effect (for those few squares). 
