Let me ask, are you duplicating complete Pages over in the Organizer?
Otherwise, a simple thing to try is to Reset Opus to its defaults. You would lose customizations of the Editor/Workspace, but it might clear-up minor glitches.
viewtopic.php?t=471&highlight=launch+alt+ctrl
I myself do not know of the particular problem you describe.
If you have created multiple Script Objects on a page, and somehow have same named functions in more than one script object... it could confuse things. A similar problem could arise if Opus is trying to executing code from multiple script objects... immediately on Page opening (and somehow there are conflicts).
Another possibility is having named host objects and variables with same names.... that is a 'no-no'.