So I want to have a transition at the start of the menu, i thought that if I just made a video in after effects with the transition at the front and the menu background afterwards and set a loop point when the menu portion started, that would do it. Problem is that I don't want my buttons to appear until it hits that loop point, Encore is just disabling the buttons but leaving them on screen until it hits the loop point. Is there a way to have the buttons appear when it hits the loop point?
If the button graphics are part of the AE animation (fading up/flying in, etc.), then you need to make sure the button layers in Encore are all hidden by poking out the eyeball for the layers in the Encore Layers panel.
If you are relying on Encore for your button graphics, then you can:
1. Put the transition video into a timeline and then link the end action of the timeline to the menu; or
2. Put the transition and initial menu animation up to the loop point into a menu with no buttons, and then link the end action of that menu to the working menu.
Which method you choose depends on the content of the video clips that are used and the effect that you are trying to create.