Trying again with the screenshots...
Here is master C (just the header with the title/chapter + page number):
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Here is master B (just the footer with the page number):
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This spread should have master C on the verso and master B on the recto. Neither header/footer is showing up.
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Masters are applying just fine in new docs.
~Valerie
The first thing I am thinking is that the pages somehow have overrides and the overrides need to be removed to you can see the Master items.
You can select items that are on the Master with Cmd+Shift+Click and then they can be deleted. This would cause them to not show, and that would be an override. (The can also be done from the Pages panel menu.)
The overrides can be removed using the Pages panel menu and then you will once again see the items on the Master.
Try this first, as it is the most likely and the easiest to fix.