To answer the question, no layouts do not run when switching between them.
You can:
1. Not use layouts. Just use layers and visibility, or different positions on the same layout. This may have memory issues, as the one of the main point of layouts is to unload unused resources between layouts. It might not though, depending on the scope of your game.
2. Add "catch up" code to the start of your layout. You can check how much time has passed since you left the layout, and simulate/fast forward the progress that should have passed while you were not on the layout.