From this OP comment:
although the site itself deregisters the main wordpress jquery handle and the re-registers it to point to the google cdn verrsion
That is your problem.
The problem isn’t an issue with WordPress 3.5 per se, nor is it a problem with Plugins.
The problem is that you’re deregistering the core jQuery version (itself an inherent problem, that causes all sorts of other problems), and you’re probably doing so at an action that causes other scripts not to be able to grab jQuery as a required dependency.