Send me the project and an explanation of what is happening to you exactly, because from your explanation I can’t see the problem.
If you mean that your scene plays a seamless animation that looks fine when you place the same scene on the left page and on the right page, that animation can “break” when turning pages because, during the animation, the script has to take the scene out of the current viewport (slot1 = left page, slot2 = right page) and move it into slot3 (the initial face of the animated page), in order to configure the other slots with the correct images.
That movement of nodes can break any seamless animation that was formed by two pages together.
If you mean something else, send me the project and I’ll take a look at it.