Great episode, guys. Both of Justice League and of World's Finest Podcast. Couple of comments:
Mike, my take on the EM distortion being noticed in the alternate reality is this. The electromagnetic disturbance was caused by Vandal Savage sending the computer back in time, which happened in the "real" timeline. This created the alternate reality. As the alternate reality was an offshoot of the real timeline, however, timeline-altering events would still register in some way, at the appropriate point in the timeline. So for the alternate reality to ever exist, the distortion has to occur at that point in time, even though the event triggering it technically doesn't. It's a chronal ripple or something. Maybe that doesn't make any sense at all, but then neither does any time travel story if you think about it too hard. I actually always felt the bigger plothole in the first episode was "Oh, we probably aren't affected because we were shielded by GL's ring," which never really felt like a strong reason to me. Which is all forgiveable because it sets up such an awesome story.
Second, the Blackhawk music. I'm fairly sure that I have heard or read that the (awesome) Blackhawk theme used here is a classic theme from the brief Blackhawks radio series. In fact, I think it's mentioned on the DVD commentary for this episode. A quick Google and Wiki search turned up no information about this, so I may be completely wrong, but I think there's a bit of history to that tune. I totally agree that the animation in the Blackhawks sequences is some of the best we see in this series. I haven't watched this in a while, but there's a shot in there that's a close-up of Blackhawk's face, strobe lit by his own machine gun fire, that I have always loved.
Also, since it's relevant to the ongoing discussion, I freaking love the Human Torch homage. So cool.