The default menu comes from
Packages/User/Default/Main.sublime-menu, so this is likely the reason for your woes.
If the purpose of this file is to add extra menu items only, you can edit it and remove everything except the ones that you wanted to add. If you meant to override the default menu entirely it should be stored as
Packages/Default/Main.sublime-menu (i.e. not in that folder inside of your
When Sublime loads the resources for e.g. the main menu, it collects all of the files named
Main.sublime-menu from all packages and combines them together into a single file.
In contrast, since the
Default package is shipped as a
sublime-package file, creating a folder named
Default in the
Packages folder and putting
Main.sublime-menu inside of it tells Sublime to ignore the version of the file as it exists in the package and use your copy instead.
This page from the Unofficial Documentation covers this in a bit more detail.