ascpete, my roots are definitely aerated, to an extent. All my cups have holes in them on the bottom, and slits in the sides. I was having some problem with leaf rot, or at least browning, so the past several days I've kept the bin cracked about 3/4" and a fan blowing on it from the far side of the room, so I should be getting some circulation, albeit it probably isn't great down there at the bottom of the bin.
If its a pretty normal thing for the exterior roots (getting exposed to excess water, temp changes, etc) then I don't think I have too much to worry about.
Elin, the soil is just moist perlite.
I think my solution stays the same though...just don't water/fertilize them for awhile to let some of that moisture get out. They should use more moisture as their leaves develop anyways.
Thanks for the insight everyone.
-Brett