I recently did a clean install of Eclipse from the tar ball (eclipse-SDK-3.7.2-linux-gtk-x86_64.tar.gz) and when I went to "Help > Install New Software...", entered the URL of the site to install a plugin from, it failed to actually list any entries. If I click on "Select All" then it indicates that items have been selected although they don't display on the list.
This does appear to be similar to Bug 290395. However, I have already tried the fix that was suggested (i.e. export GDK_NATIVE_WINDOWS=true), but that hasn't helped with the problem.
Not sure exactly how this was solved, but it appears that by deleting the Eclipse directory along with all of those that were created and the workspace directly, the issue was resolved upon doing a fresh install and start up of Eclipse. The issue was likely still due to the GDK as mentioned in the question, but the exact reason is not obvious.