Also please try http://download.jboss.org/jbosstools/updates/JBossTools-3.3.1.Final.core as update site to install any component of JBoss Tools. I just verified bundle mentioned in original post. I downloaded it form http://download.jboss.org/jbosstools/updates/JBossTools-3.3.1.Final.core/plugins/org.hibernate.eclipse.console_3.5.1.v20120715-0252-H98-Final.jar and used md5sum to check MD5 hash and it matches expected one.
eskimo@dgolovin-desktop:~/Projects/jbds-build/jbosstools-src$ md5sum ~/Temp/org.hibernate.eclipse.console_3.5.1.v20120715-0252-H98-Final.jar
2b8a871d38aeb31ca6cab8dc99111be4 /home/eskimo/Temp/org.hibernate.eclipse.console_3.5.1.v20120715-0252-H98-Final.jar
It works fine for me for all mentioned scenarios. It could be a problem with proxy server or cache.