The Tools menu is ALWAYS there in FileMaker Pro Advanced. This is because if you totally screw up your Custom Menus, you need to be able to reset things back to "[Standard Milemaker Menus]". So it's not a bug, but a feature!
On the other hand, the Tools menu does not exist in ordinary FileMaker Pro. That's because the Tools menu contains "developer" functions for developers to use - the ordinary users won't have it, so they are imprisoned in "no menu hell" if you stuff it up :-).
Bottom line: check what ordinary users see by logging in using ordinary FileMaker Pro. You're the developer, using Advanced - the users are not.
Fantastic. Thanks for this great help. Looking forward to also becoming a