shanan- When you say “linked via buttons”, do you mean buttons on a menu, or are you using buttons on the remote control?
There are some limits as to how many buttons you can have on a single menu. I think the limit is 36, although 16:9 menus are even more limited (18 buttons?).
If you’re using overrides, Encore also seems to have some sort of internal limit on the number of buttons that can link to a single timeline. (For example, if you have a menu transition video play when each button is pressed, then the timeline plays.) If memory serves, the limit was 42. If you have more than 42 buttons with overrides linked to a single timeline, it plays the timelines in the wrong order.