Small comment: map is huge in kb.
Actually, the waits cause this to happen. As you see, when a wait initiates, it causes the SC engine to scan all triggers to see if their conditions are fulfilled and runs them if they are. If there is a wait inside the second trigger, it will wait until that is then before finish the first wait in the first trigger. And since there is a wait at the dark archons, it will cause the second trigger to run, and wait, and when that finishes, wait for the first wait to finish, then repeating with the first trigger again.
In conclusion I'm basically saying:
It's the waits causing the problem.
Try using this map for reference:
http://www.staredit.net/index.php?download=2195