With this module activated the menu item level settings for the Menu Minipanels module disappeared. Other modules might be affected as well.

Proposed resolution

_menu_attributes_form_alter starts out with assigning an array to $form['options']; If the new options are merged with the existing $form['options'] array, previously added fields won't be cleared out. This could be done either by something like array_merge(); or just individually assigning the values like so:

  $form['options']['#tree'] = true;
  $form['options']['#weight'] = 50;

Remaining tasks

There might have been a reason beyond simplicity why it was done this way, so that should be addressed.