I HAVE SAME PROBLEM TOO! I use an other template than default, and the pictures don't open in thickbox.
" I have the exact same problem after upgrading, JQzoom works fine, but thickbox doesnt, when you click on the image nothing happens, and when you click on the thumbs it opens the image in a blank window."
ANY SOLUTION PLEASE? I TRIED A LOT OF THINGS BUT DON'T WORKING!!