Check this forum thread out:
Original Schedule Files Now Available at Retrosheet!
Look for the posts by fearofmimes on page 3 of the thread; he did some fairly extensive tests on doubleheaders.
In a nutshell, start times have no effect on the doubleheader results, as the game simply processes one game of the schedule at a time. The pitcher use issue you're having relates to fatigue issues, where the fatigue generated by the players playing in a game is only updated by OOTP at the end of a day rather than at the end of each game. As a result, a pitcher sometimes winds up pitching both games of the twin bill because his fatigue wasn't updated after the first game.
By the way, I've already got ALL of the actual MLB schedules and a ton of the minor league ones. Just check out the Retrosheet web site to see what has already been made available officially.
Now we just need to convince Markus to support the Retrosheet schedule file format in the OOTP6 schedule importer/exporter...
