Javascript (?) not working in second blog on server

Hi;

I’ve got two wordpress blogs on the same server, one as root and one in a subfolder. The root is version 2.9.2, but the subfolder (which is brand spanking new) is 3.0.4.
Ever since I installed the new version, it’s been acting a bit funky with the javascript elements. (Drag and drop, the WYSIWYG editor, the more complicated uploader, etc.) I’ve tried a couple different things I’ve seen around on the internet (Disabling plugins, using the google libraries instead on the built-ins, etc) but haven’t been able to quite get it right. It’s usable, mostly, but I’m giving this off to a different department and I don’t want to freak them out. (Also, the not being able to drag and drop widgets is DEEPLY ANNOYING.)
Now, the root blog is working just fine, so I’m wondering if I missed a file somewhere, but I mostly just unzipped the wordpress files in the subfolder in my htcdocs, and it was good to go. (after setting up the sql tables, etc, of course.) I’ve never set up a second blog on the same server before, and am wondering if I missed something.

Thanks;

Any suggestions would be great;