Thanks torog. I got off my lazy ass and posted this question on overgrow. I've come to the conclusion that I have a water and/or pH problem (not sure yet, because my pH testing strips are still in the mail), but I'm pretty positive it's a water issue because I've also been having poor germination results using the "soak in a cup overnight" method.
Also, I'll be sure not to use transparent containers anymore
~007~