I'm running WP 3.4.2 on a VPS. When I first moved to this VPS server and imported all my WP data from the old, the menus worked fine. However, for some reason, I cannot edit/add to the menus, and some items have been deleted. No matter how many times I try to re-add those items, they won't appear. WP does not report any errors. When I add them again, and click the "Save Menu" button, after a long pause (30-45 sec) WP simply says, "The Main Menu menu has been updated." But the new items are missing, both from the site menus and from the WP menus setup.
Originally when I first moved to this VPS there were 9 menu top-level items, about about 90 submenu items -- about 100 menu items total. Everything displayed correctly.
Now I am limited to 88 menu items. I can only add a menu item by deleting another.
I'm not sure when this problem started, because we don't edit the menu often. It was noticed for the first time yesterday that some menu items had disappeared, which may coincide with someone adding or editing a menu item. But we've been running on this new VPS for about a month.
I found in another forum discussion a reference to suhosin which can cause menu limit problems in WP 3.x, but that is not part of our PHP installation.
I've tried Safari and Firefox (OS X). Same results with both.