Without seeing any code, ensure that your index.html page is setup as the master (if that’s your design schema). With your HTML semantics, make sure you’re setting up your main tag after your nav so that you can assign the Site Content action to the main tag. Save it and re-export your theme, it should follow through on those pages to show the nav working as intended. However, check the setup of each page that has the nav menu to make sure it doesn’t contain the wrong page information – it’s possible that interior pages may accidentally be marked as master pages due to your workflow.
It turned out that I wasn’t setting the header as a reusable template part. For some reason I thought Pinegrow would be using it automatically for other pages based on index.html, but this doesn’t make sense now that I look at it again.