I'm not quite tracking with everything you are asking about, but I do have some insight ("guesses") that might help you.
It might be that addon 'init' EHs work just like init.sqs. Init.sqs is called on the map briefing screen, just before the mission starts, and it will proceed until it reaches any sort of a delay.
The same might be happening with your addons-- their init scripts are running on the map screen, right up until they hit a delay. At which point it stops, waits until the briefing is over, and then keeps on going.
As for conditions not working properly: You need to be pretty careful when using conditions at the very start of the game (before any delays). It would all depend on what your condition is, but OFP might be running into the condition before certain variables/units are initialized. I know there is one huge PITA bug when it comes to when OFP initializes arrays.