This is incredibly confusing for users that work within multiple agile boards. The selected ("current") Structure is the one that shows up even if you navigate to another agile board. The tool should retain the context of the agile board that is selected and choose the appropriate structure as it would if you select a structure from the Structures menu.
Annoying oversight or defect?
First, my apologies for the late response - we monitor this site for questions tagged with our product keys (in this case it's addon-com.almworks.jira.structure for the Structure plugin) but anything that's not tagged is liable to be missed. In case of support requests or any questions that require the direct attention of our team, please use our public JIRA or write to firstname.lastname@example.org.
To answer your question - the Structure panel in the issue details view (and the Agile sidebar) is designed to retain the same structure board when you navigate around issues. This is for convenience from the point of view of a Structure user (it would be confusing if the structure in the panel kept changing).
Currently there is no way to tie a specific structure to a specific agile board. If you'd like us to add such a feature, please could you make a feature request on our Structure UserVoice forum or our public JIRA.
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