Yes, events no longer process on layouts that are not active, effectively "stopping time" for that layout.
As others have mentioned, you'll need to add events for the time to "catch up" to current time, by using the expression to find out how much time has passed since you left the layout.
Another option is to not use layouts in the first place, if possible for your game. You can use layers instead, and hide visibility (and remember to account for controls or input so they do not work on invisible layers). This way, all your "scenes" are actually on the same layout and running, just hidden.