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Perhaps you can try the following suggestions (if you haven't already). They are basically guesses, but without a file to investigate, it is difficult to pinpoint a cause. Keep in mind, you can test your Project file using the "Detach from Central" option (for Workshared Projects only) when opening it so you don't risk messing up your Central file.
- Ensure that you are up to date on Service Packs and fixes.
- Entirely recreate the problematic Section View. Do not duplicate the View or Copy the Section.
- Create a View Template from a correct Section View and apply it to the problematic one.
- Entirely detach and then reattach the Structural link.
- In a new Project, try recreating this issue using the same Structural Link.
Also note that sometimes, problems are isolated to a single Project file and opening a Support Case is the only course of action (although that does not guarantee a solution).
Corey D. 
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⁞|⁞ Please use
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