It's no use to set CheckConfigurationPermissions to false, because the default configuration (./libraries/config.default.php) is read and _PROCESSED_ before ./config.inc.php.
This causes problems on mounted NTFS volumes under Linux.
(I'm currently using 3.1.3.1)
Fixed, see http://phpmyadmin.svn.sourceforge.net/viewvc/phpmyadmin?view=rev&revision=12345