Redirect problem on custom domains

I've got WPMU going with a root site id=1, buddypress on id=2 and some subdomains running on one of three subdomains:
1 = maindomain.com
2 = buddypress.maindomain.com
3 = client1.maindomain.com
4 = client2.seconddomain.com
And these are working fine. But when I try and add custom domains using the domain mapper plugin, e.g. id 5 = clientdomain.com, when I browse to clientdomain.com I'm instantly redirected to site 2, buddypress.maindomain.com.
Any ideas? Not sure if it's related but I'm using nginx instead of Apache (in case it's a rewrite rule problem?)
Thanks!