Thank you for your post.
With Instant Web Publishing, you are using a browser to access FileMaker Pro records, and FileMaker Pro is doing its best to give that information to the browser. Assuming the Instant Web Publishing users are logging in with privileges to View the Related Fields, FileMaker should display that information. Since the fields are not showing, it could be caused by a corrupt layout.
Try creating a new layout with the Related fields showing (do not duplicate a layout). See if this information is showing. If so, then remove the Related fields from the suspected Layout and add the fields back again. This will reset the object information. See if this is visible with Instant Web Publishing.
Any additional information you can provide may be helpful in determining why this is occurring.