I think they cut out more from the second episode. If they didn't, then I don't understand how they could interrupt it with Bush's speech and still end it at 10:25, approximately.
It was intended to end at 10. The only really relevent event was showing how Clinton's lack of response in Somalia led directly to Ben Laden deciding that America was a Paper Tiger and could be attacked with impunity.
Rush stands by the "one minute cut" statement. He also said the movie was planned for 5 hours when ABC planned to run advertising. They were unable to get advertisers, so ran it without ads. This left them 20 min. short each night. The first night, Nightline's Rat talking points completed the hour, and the president filled the extra time on the second night.