I had the same problem. I did not have pre-existing menus, but newly created ones had the same symptoms as you described.
In my case, the problem was a ill-defined table wp_terms. It was missing the AUTO_INCREMENT flag on the column term_id as well as all indexes and the primary key.
I can only assume that the update process messed up at some point in the past. I run a pretty ancient installation which was originally set up in 2005.
The following change fixed the problem for me:
ALTER TABLE `wp_terms`
CHANGE COLUMN `term_id` `term_id` BIGINT(20) UNSIGNED NOT NULL AUTO_INCREMENT FIRST,
ADD PRIMARY KEY (`term_id`),
ADD INDEX `name` (`name`),
ADD INDEX `slug` (`slug`);
I would recommend comparing your schema against a current schema though. wp_term_taxonomy might be involved as well (wasn’t in my case).
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