It should save the state with all variables. All I can think of is that it isn't saving at the point where you think it is or on load you have events that change the variables instantly so you could never tell.
When loading the Saved Slot, the "On Layout of Layout" executes again? I don't think so since it would restart the global variables, etc.
As you can see in this video, at the top the areas I show requires 5 woods the first one, and 5 men the other. After merging both icons and assigning to each area, now they need 4.
The red dot indicates the game has been saved. At that point I already have 2 new heads on the grid.
When leaving the game and continuing, I see the 2 heads, the music continues from where it saved, etc. But the required wood and man are still 5.
Those values are just instance variables that hold a number, nothing special :S