 solved
skins per domain or global problem is solved within release 5.0.9.
example:
zmprov md "mailtest.testdomain.ch" zimbraSkinSecondaryColor "#cfe2ff"
zmprov md "mailtest.testdomain.ch" zimbraSkinBackgroundColor "#f2f2f2"
zmprov md "mailtest.testdomain.ch" zimbraSkinSelectionColor "#ebf0ff"
zmprov md "mailtest.testdomain.ch" zimbraSkinLogoAppBanner "/zimbra/skins/skinname/logos/AppBanner.png"
zmcontrol stop && zmcontrol start |