scenario files and 'at-start' stacks ... duplicates?

I’m working on a module for a game designer. He wants to limit players to only the counter pool available in the actual game. This is being done through ‘at-start’ stacks on private windows. He also wants to allow the players to select scenario setups from a drop-down menu. I’m trying to support this through startup vsav files. When we load the scenario from the scenarios dropdown the counters used in the scenario are also still available in the ‘at-start’ stacks. However, if I load the same scenario by clicking the LOAD command and select the vsav file from my computer’s file system, the duplication does not occur? Is there anything I can do to overcome this?

Also when opening a scenario file (embedded) from the the Scenario Menu, text entered in the scenario section of the Notes cannot be seen. When using the LOAD command, the notes are visible. Is this a bug, or did I miss something?