Permalinks not working – save in yoast fixes page, breaks posts

I’m having a strange problem that I think it is related to Yoast and the recent 3.3.2 update (also happening when I updated to 3.3.1).

When I visit a page that uses (or is supposed to use) a custom page template it appears to redirect and pull in the content of the parent page template.

I looked at all of the settings in Yoast and when I make a change in the Yoast > Advanced > Permalinks page (any change) and then save it, the page correctly pulls in the custom page template.

However doing this breaks the permalinks for my posts and taxonomy pages (and possibly others) so that when I open the posts or tax URLs (even from within WP Admin) they come up as “page not found”

Going into WP Settings > Permalinks I simply click “save” to resave and it fixes the posts/tax pages but then breaks the page using my custom page template to again pull in the parent page template’s content.

Any ideas on how to fix so I can stop this cycle?

Thanks in advance

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