Around line 196 of the \moodle\blocks\admin_tree\block_admin_tree.php file the folder for the Moodle admin directory is still hardcoded instead of using the variable called from the config file (i.e. $CFG->admin). This causes errors for those configurations using a different folder.

$this->content->footer = '<div class="adminsearchform">'.

*** '<form action="'.$CFG->wwwroot.'/admin/search.php" method="get">'. ***

'<input type="text" name="query" size="8" value="'.s($searchcontent).'" />'.
'<input type="submit" value="'.get_string('search').'" />'.
'</form></div>';