No, I meant a Multisite network. Anyway, it sounds like that doesn’t apply in this case.
I don’t think W3 Total Cache could be the problem, at least not on its own. That’s a very popular plugin, and I would probably get a lot more reports like yours if there was a conflict between these two plugins. Is there any other cache involved? Database caches would be particularly relevant.
Also, there is another approach we could try. On a regular site (i.e. not Multisite), this plugin stores the admin menu configuration in the wp_options table, in an option named ws_menu_editor. Please check this table for errors (most DB management tools have a button for that), verify that this option exists, and that there is exactly one copy of this option in the table.
Assuming all that goes fine, can you think of any process or plugin that might change this option, or wp_options in general? For example, if there’s something that does a search-and-replace on the table, it could inadvertently corrupt the menu configuration, which would cause AME to reset the configuration. In this case, the plugin would reset the configuration to the default values, not to an older custom configuration.
