Menu Not Displaying In Subdirectory 404s

I had this issue a while back and fixed it easily enough by switching my permalink structure to /%category%/%postname%/, which still works fine on top-level 404s. You go to mysite.com/404 and you can see the menu normally.

However, if I add any intermediate directory to the address, I’m having the same problem. E.g. mysite.com/404 works fine, but mysite.com/wp-content/404 does not.

I’m guessing it’s another permalink issue, but I don’t really know what it wants at this point. I tried setting .htaccess to 777 and resetting the permalink structure (since that was recommended by another thread), but that didn’t help.

Thanks for your help!