Care must be taken when tracing rooms on multistoried projects; i.e. when tracing rooms above/below other rooms.
To ensure this, always check that you have set the Active Floor to be the floor where you want to draw the room.
To do so, go to the project tree on the left side of the screen, and select the floor you want to work on.
Right click on the relevant floor and set to Active as shown below:
Now, the floor is active and you can trace rooms at that elevation.