I used http://www.ac6-tools.com/Eclipse-updates/org.openstm32.system-workbench.site/ as the install site and selected only 201611241417 versions. (I had to remove “Show only the latest versions of available software” in the Install dialogue box. This seems to install correctly on Ubuntu 16.04.
I saw this problem when I tried to install updates - similar to http://www.openstm32.org/tiki-view_forum_thread.php?forumId=7&threadId=4205
Hope that helps and happy new year