I tinkered a bit with it and came to the following conclusions:
It's not the layout that's getting resized, just the objects in the layout that have some effect applied to them. I added a sprite object to layout 2, and pushing buttons had no effect on it. If the it was the layout that was changing size, it would affect the sprite too.
I think there's an issue with using effects on objects in a layout that is inside a layout object.
For the record, I used version 99.2