menu from subsites link to main site

WP 3.1.3 multisite, Domain Mapping 3.0.4, other plugins include marketpress, membership.

Permalinks set to Day and Name.

head site is domain1.com which has some pages and a custom menu.
subsite 1 is domain2.com which also has pages and a custom menu.
subsite 2, 3, 4 ditto

The problem is that the links from the menu on subsite 1 etc all say they are linking to domain2.com etc but in fact try to load the main page of domain1.com.

Is this a permalinks issue?

Or do I need some other menu manager?