I think this started when I upgraded WP recently - probably with 3.1.2 - upgrading to 3.1.3 didn't fix it.
I have three lines of code:
I've added to my header, both before and after the wp_head function and I also tried it in the footer but these three lines are only added to the displayed page if I am logged into the WP admin area and the grey bar is at the top of the page. Otherwise they are missing and the jquery functionality is broken.
I know the path to the files is correct, as the link to the .js files when I'm logged in and the code is actually shown.
Help, it's doing my head in.
An example page: http://www.cucocreative.co.uk/client_folio/the-dungeons/
I have set up a guest subscriber account so you can see what I mean: