After applying the fix you mentioned, the layout of menu items is fixed, but the function is still broken. Configured restrictions are not saved, thus another plugin to role based restrict visibility of menu items is necessary.
My reply in your 3.0 support forum remained unanswered though.
By following the recommendation with the WP login page, also the WP registration page gets again useable circumventing Pie Register.
I solved that with another third party plugin to retoure the system registration link to the plugin registration link. It would be great if there would be two options in the settings, forbid system login and if NOT selected forbid system registration.