If you could post your capx, it would be easier to spot on what went wrong.
From the sound of it, I'd say select your layouts in the "Projects" tab and make sure that their "Event sheet" property links to the intended events sheet.
This might be a first thing.
Another thing is the order of the layouts.
If you have some variables and code for these variable set in event sheet 2/layout 2/Menu in you case and that you start directly the program on layout game, the whole code about the variables won't act indeed, since the layout they are in never got initialised.
Make sure that the correct layout is selected as "First layout" property of the project itself.