Hey Joe. Thanks for the suggestions. I can address a few of them...
I did think it may have something to do with the chilling method. Normally I cycle through the chiller a few times and the resulting wort is quite clear. I only did it once here (which didn't quite get me down to pitching temp) but maybe it's highlighting a benefit of using a good chiller.
I did not check pH on either.
The boiled wort was a higher gravity, but I did some math and topped it up with water until it hit the OG of the non-boiled beer. They both started at 1.034. Both finished at 1.004 too. That's 88% ADF which is high for 002, but I added sugar so that's not too surprising.
I do have a two-year-old daughter and those are just foil caps covering the fermentors. She may have tossed something in there!
I should add that the non-boiled beer dropped clear much faster than I normally get with 002, but then again I've never skipped the boil or had such a low OG with this strain. Now that both beers are kegged and in the fridge, maybe their clarity will change. I'll keep this thread updated when I find out.