From: Covington, KY, USA
I'll add a couple points, too.
1) I believe armies will not attack if they are the only force in a region (read: stack). That's why it appears that sometimes they don't attack (unless attacked, of course). Now, a separate stack with attack orders may force the issue. That's why in defensive situations (eg, Alexandria, VA) I always have a separate stack (a brigade w/out a leader) set to orange/orange.
2) the above folks are right: piecemeal entries to a region are a great risk, even if they are the same army. Using coordinated movement helps, but still no guarantee that they'll all arrive at the same time for the battle.
3) Johnston appeared as leader for both first battles because he was present for both (even if not leading the stacks in battle). You'll often see this where a senior general (even in adjacent regions, I've noticed) appear as the primary leader. He was not present for the last, I suspect, because he had vacated the region and was green/green. That left poor Gustavus to get body-slammed.
4) just because all players are orange-red/(blue or higher) in a zone does not mean a battle will occur, or if one does, all stacks will participate. Such is warfare in the 1800s.