Menu settings missing from all node edit forms Apart from what I mention in the title, there are also a couple of other things that give me the impression that they may be related to the same issue:  


Can’t add link to any menu from
admin/structure/menu/manage/my-menu/add. What does happen when I try
to add a link to any menu is that it ends up in the Navigation menu
that comes OOTB.
Can’t assign any menu to taxonomy menu. Having taxonomy_menu
enabled, I noticed that when configuring the vocabulary via
admin/structure/taxonomy/gamma/edit  there is no possiblity to assign
any menu as taxonomy menu. The only option in the drop-down list is
=NONE=


There is also A list of modules on which I did this series of events: disabled the module, cleared cache, checked if the problem persisted (which it obviously did), and enabled the module again: 

Here is the list:  

Big Menu
Jump Menu
Mysite configurator (custom)
Mysite (custom)
Store locator (custom)
roleperm_import (custom)
mforms
mforms example
Menu Block
Menu import
Menu translation
Taxonomy menu _ custom paths
Taxonomy menu
Administration views
Backup and Migrate
Taxonomy translation
Menu translation

Needless to say the core Menu module is enabled.

Went looking on the internet, found this issue (https://drupal.org/node/358844) on drupal.org but this was drupal6 plus the big problem there was that the everything menu related seemed to be missing. The solution there was that menu permission weren’t right, which I have verified on my site that they are ok.
"Menu settings missing from all node edit forms"


You need to enable the menus for use on each content type. This can be achieved on pages via Structure->Content type->Basic page, then click on the "Menu settings" vertical tab and toggle which menus should be enabled.

Also, if you're using the revisioning system in core, or any kind of workflow type module (workflow or workbench), unpublished pages in the menu won't show up in your list of menu items in Structure->Menus->Main Menu (for example), as well as the obvious rendered menu on the front end too.