Comment 4 for bug 530456

Version 17, now available for download at http://launchpad.net/mysqltuner/2.0/mysqltuner-2.1-rev17/+download/mysqltuner-2.1-rev17.tar.gz has the workaround in place of having different config files (one with table_cache, one with table_open_cache).

I am leaving this bug open because you are correct, there should be a better logic system in place for similar issues (for instance, "if InnoDB is disabled don't bother checking the buffer pool size").