I also have this problem. Actually, plugins are not loaded, and therefore the tools menu shows much less items it should. However, a link from /usr/lib/ggobi/plugins to /usr/share/ggobi/plugins solves the issue.
I also have this problem. Actually, plugins are not loaded, and therefore the tools menu shows much less items it should. However, a link from /usr/lib/ ggobi/plugins to /usr/share/ ggobi/plugins solves the issue.