Every time one of these plugins is updated I freak out. I use both Multi-Domain and Domain Mapping on a few sites. Domain Mapping provides a bunch of capabilities that ease the ability to use custom domains for individual sites - but Multi-Domain is just as essential to a site that provides multiple domain mappings. Both are very nifty stuff. Thanks.
But both require sunrise.php to be setup specifically for them. Multi-Domain provides a sunrise.php that's compatible with Domain Mapping - but Domain Mapping does *not* provide a sunrise that's compatible with Multi-Domain. After a release of DM it can be quite a while before there's a Multi-Domain update.
Ideally, DM would include a sunrise.php that's compatible with Multi-Domain. If not, release an update for Multi-Domain at the same time so we can ensure that a compatible version of sunrise.php is installed.