Need more test on $standardtemplaterootdir .

$standardtemplates isn't an array : can add a line in admin.php line 743 : $standardtemplates[]=$file;

But best is to use
$standardtemplates = array('default', 'basic', 'limespired', ....);

But then when try to renaming not default template but a template in $standardtemplaterootdir : need to use
$olddirname= sGetTemplatePath($copydir);
and not
$olddirname=$usertemplaterootdir."/".$copydir;
at line 277 (and test if it's not a default template)

Can this be a duplicate of http://bugs.limesurvey.org/view.php?id=4321 ?

Yep right,

need to acces to SVN or wait for beta3 ;)

Maybe Thibault will release another beta today. In general SVN is the best long-term solution.

1.90 beta3 release