Local HSQLDB started using hsql ant target is shutdown cleanly when Tomcat running uPortal is shutdown.
See PBOOK-76 for the cause.
The fix will depend on a new release of the BookmarksPortlet that will include a change to the default spring applicationContext.
If you want a temporary fix for your workstation, I've attached a patch that comments out the cause for the shutdown in an "overlay" configuration. This patch should not be checked into the subversion repository for uPortal.
Fixed by updating to bookmarks portlet 1.0.9