Sorry Klas, I wrote wrongly addMetadata but I am using setMetaData like you say and it does not override existing values:
$doc->setMetaData('Description', 'newvalue');
adds a new meta data row (since first letter is capital so it is considered as a new property) while
$doc->setMetaData('description', 'newvalue');
does nothing - old meta description remains what it is...
any guess? Thanks!