Not quite sure where the problem is without looking at a capx.
Obviously when you a have a larger screen there are more pixels to render which requires more computation. Do you have any webgl effects as they would need to do more work on a larger resolution?
Have you made any search or resize algorithms based on screen size?
What I normally do in this kind of situation is to make a copy of the capx and start systematically disabling bits and previewing the results in a hope to finding the cause. This at least helps to isolate the problem into a capx you can potentially share.