It MAY be due to the fact that the working directory ($wd) on which Tomcat is running is $CATALINA_HOME.
this might be the case if you run tomcat by issuing the shell command from $CATALINA_HOME (something like "cd $CATALINA_HOME; ./bin/startup.sh").
Since in my opinion it's not straightforward to depend on the working directory to locate my working datastore, I solved the problem editing WEB-INF/components.xml in the drools-guvnor.war archive, uncommenting the "repository.root.directory" property (as suggested for production environments):
<!-- JackRabbit -->
<!-- the root directory for the repo storage the directory must exist. -->
Hope this helps. Cheers,