I have the following error:
/*! jQuery Migrate v1.0.0 | (c) 2005, 2013 jQuery Foundation, Inc. and other contributors | jquery.org/license */
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Uncaught TypeError: Cannot read property 'value' of undefined
//@ sourceMappingURL=dist/jquery-migrate.min.map

Got this using this plugin: http://www.herdboy.com/all-free-stuff/item/jquery-migration-plugin-for-wordpress, read about another plugin not working due to jquery deprecating functions, so I figured I’d try it. There’s no error when that plugin isn’t running.

It’s something with the database, not the files. I setup a new install of wordpress, and pointed it at the old database, and it has the same problems. Point it at the new database, and the menus work properly. I’m working on porting all of my content, but it’d be nice to not have to