The Menu plugin in the current version does always show the complete number of stories in a topic instead of the number that the user can actually see with his current permissions. To Fix this please open the file functions.in in the directory geeklog/plugins/menu and change the line 455 from

$rcount = DB_query( "SELECT count(*) AS count FROM {$_TABLES['stories']} WHERE draft_flag = 0 AND date <= NOW() AND left(tid,length('$tid')) = '{$tid}'" );

to

$rcount = DB_query( "SELECT count(*) AS count FROM {$_TABLES['stories']} WHERE draft_flag = 0 AND date <= NOW() AND left(tid,length('$tid')) = '{$tid}'" . COM_getPermSQL( 'AND' ));

then the number is correct.

Both of those lines are the same, Am I missing something?

Sorry, must have forgot to submit the last edit. It should be ok now.