URL dropping subdirectory when entering from certain pages

When I click one of the menu options on the left hand column of the store page or enter the store from an individual product linked to from a blog post, every subsequent category or product in the store results in a URL that is missing the /store/ subdirectory. This means that when I copy the URL from the address bar and use it as a hyperlink or send it to someone, when they click that link, it takes them to an error page on my site. If I use the store option from the top menu on my site, all the links render correctly and I don’t have this issue. I have spent hours trying to change settings and figure out what is causing this discrepancy. Does anyone have any ideas as to why using the left menu (which is hard-coded with a custom url option) to enter the store would result in URLs dropping the /store/ subdirectory? Any suggestions would be greatly appreciated!

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