I think the cause is in the classes/files.php.
in the //DELETE THUMBS sections this foreach is added:
foreach(JFolder::files($dir) as $file)
When i check the JFolder::files function at
docs.joomla.org/API16:JFolder/files there is a default excludefilter:
public static function files($path, $filter = '.', $recurse = false, $fullpath = false, $exclude = array('.svn', 'CVS','.DS_Store','__MACOSX'), $excludefilter = array('^\..*','.*~'))
I works when i change the foreach statement to:
foreach(JFolder::files($dir,'.',false,false,array('.svn', 'CVS','.DS_Store','__MACOSX'),array()) as $file)
I have now emptied the excludefilter, if think only deleting the second array entry is enough.