Hi Tobias,
I'm also having a problem with the javascript libraries not being loaded on the page, but I definitely have wp_footer(); in the theme: I can hook into it and add stuff to it from my functions file.
I'm using Wp-Table Reloaded 1.8 and WP 3.0.4.
I can't really give you a link to the site because it's not public yet, and most of the content will be members only, but I hope you can point me in the direction of things to look at.
The other plugins activates are:
AVH Extended Category widgets
Cforms
Event Calendar / Scheduler
Mingle
Poll Daddy Polls
Shadowbox JS
Simple:Press
Social Media Widget
Tooltip Glossary
Wenderhost Subpages Widget
Widget Logic
Wishlist Member
WordPress.com Stats
But I don't see how they would cause the javascripts not to load... only cause js conflicts after they've loaded.
Hope you can help me. Thanks!