Ran into the same issue. @Patriek is correct. The ‘taxonomies’ argument must be an array, hence the plural. E.g.
$args = array( 'taxonomies' => array( 'myTaxonomy' ) );
This corrects the error.
I only noticed this when moving a site to another server which leads me to think the register_post_type() function requires some php settings not enabled on the remote host. register_globals is enabled… any ideas what make this issue server dependent?