Structure plugin maintains a cache of users permissions with regards to each structure. In most cases, the cache is recalculated automatically, but in some cases Structure plugin may miss a change in a user's groups or roles. The result could be that the changed permissions take effect several minutes later (but only with regards to Structure Permissions). A user can force the cache to be recalculated by doing hard refresh from the browser. Typically, it's done by holding Ctrl or Shift or both and clicking the Refresh button.