Admin JS issues in 'post' & 'page' screens since upgrade

I’ve got a multisite install with two websites/blogs:
root (ie http://www.mysite.com)
subsite (ie http://www.mysite.com/subsite)

In the subsite, and only in the subsite, when i go to the post or page screens in the admin, some javascript is not loaded, causing the collapsible menus and panels to be unresponsive and tinyMCE/WYSIWYG editing to be disabled. The image uploading popup also doesn’t work.
I’ve been using FireBug to check out what’s going on, and common.js doesn’t load for these screens. Upon further investigation -I was starting to feel like Philip Marlowe here- it appears that the affected screens are missing a whole chunk of html at the bottom. Since some javascript files are loaded at the bottom of the page, that would explain a lot.

So, what could be causing this? I’ve disabled all plugins and the problem persists. My colleague who’s a developer, will return from vacation on Monday so I’ll ask his opinion too and get back to the community if we figure it out on our own.