Also remember that when you hit a break in your schedule, the round has not yet changed. So if you have round 1, round 2, break 1, round 3, round 4, etc., when you are in break 1 you are also, technically, still in round 2. Might have an effect depending on how you've created your conditions. And as stuamurr mentioned, ordering can have an effect, too.
If you want more detailed help, attach your tournament file, or just the events template. Or email them to me (support@thetournamentdirector.net) if you don't want to share them with the world.