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Do you have multiple copies of Designer Installed? Perhaps one Admin and one non-admin. That way, double-clicking on a workflow may launch one copy, but you regularly open the other from the start menu.
It looks like the Guided Tour popup that you're seeing and the Learning Guide controlled by the settings are 2 different things. The Learning Guide is a workflow that opens in Designer that helps with making your first workflow.
I've only ever seen the Guided Tour popup once or twice, and I don't know how to control it.
Maybe one of the moderators like @TrevorS can chime in with a solution.