Thank you very much for the help and explanation.
I think I am calling pause() for the timelines.
for each(var tl:TimelineLite in timelines)
if (tl != null)
The reason I also call TweenMax is because there are assorted tweens and delayed calls that are not added to any timelines.
I'm not sure what I did to cause this change, something with child timelines or tweens I think, but I found that if I do the pause before the timeline begins, it's duration increases, but if I do it during the timeline, the start time increases, but not the duration. By increasing the startTime of timelines that haven't begun yet, whenever I finish a pause, things seem to be lined up once the timeline starts. Though, now I have problems with other timelines. I'm thinking it has to do with TweenMax.resumeAll and the fact that I have independent tweens and tweens on timelines. If you could answer a couple questions, I think I can work out a solution.
Does TweenMax.pauseAll/resumeAll change the pause state of all tweens regardless of the pause state or delay of any parent timelines?
What are the differences between active and paused for timelines?
What is the effect of pausing/resuming on tweens or timelines that are delayed and haven't started yet?