I have done a lot of testing and finally isolated what I think is a bug, or at least a problem. Wp-Super Cache has a feature that clears the cache for domain mapped sites, but it only works with this domain mapping plugin.
There is a feature in the cache that allows you to "Clear all cache files when a post or page is published or updated." It does not work for the WPMUDev Domain Mapped sites. You can test it by going to a domain mapped site in the cache (wp-content/cache/cache/name-of-site). Go to th site and update or publish a page or post. On subdomain sites it clears out that folder. On domain mapped sites (with the WPMU Domain Mapping plugin) it does not clear that out. But it does work when the other domain mapping tool is used.
I don't really want to use his plugin as all of our other plugins are from y'all. Can y'all make it compatible with Super Cache?