I recently upgraded both wordpress and the domain mapping plugin. I just noticed yesterday, that all of my permalinks are in the form of mysite.mymultiweb.com rather than mysite.com.
It's a small web with low traffic, so it is hosted at hostgator.
Permanent redirect is checked. I checked primary when I added the domains. I tried deleting and re-adding the domains to no avail. I tried deleting and reinstalling the plugin and re-adding the domains to no avail. I did move the new sunrise.php to wp-content after the upgrade. Because I have cpanel at hostgator, I do have the domains parked. My name servers for the domains are pointed at hostgator. There is a DNS A entry pointing at the IP. I *think* I followed all the install instructions when I updated; I certainly tried to.
Going to mysite.com in a browser works and goes to the right place, and displays correctly to the user as they navigate. But, internally, the permalinks still show mysite.mymultiweb.com.
The web in question is winswebs.com. One of the sites in question is divorcelawyermn.com.
Any thoughts for things I might pursue would be most welcome.