I have come across a small problem in WordPress multisite. When using a mapping to a custom domain, the domain is apparently mapped but internally the site retains your main domain with a sub-domain as its address. So, while externally it may be “example.com”, internally it is still “example.mysite.net”. Usually, this does not cause any trouble but you may run into unexpected problems with more advanced stuff and some plugins may function incorrectly.
I came across this when trying to configure Facebook with Social Networks Auto-Poster (SNAP) plugin. The plugin will issue an OAuth request to Facebook but the request fails because the plugin uses the “example.mysite.net” instead of “example.com” as you would expect. So Facebook understandably rejects the request to authorize. And this same thing may happen in other places.
The site URL comes from the database, options “siteurl” and “home”. Fire up your favorite SQL tool and head for the database. Find your table wp_XX_options where the site in question is stored (XX being the id of the site, they simply get numbered from 1 up). Change the two options to the correct URLs and things should start looking up.
Remember to change the URLs back to “example.mysite.net” when you remove the domain mapping.