fixed the problem - for all facing similiar problems:
1) when setting up more domains for mapping: be sure to check the primary checkbox
2) Editing the WPMS sites: check if you set the "home url" to your new domain
Hint for german users: in the german WPMS Version the Networkaccount has a pretty unlucky translation for the sites. Pages and Sites are both translated with "Seiten". So be aware, that the "Seiten" within the Network Account are the "Webseiten" where you can edit all preferences.