I was having a problem with domains showing up as a sub-domain to the main site for our users in admin, which caused some confusion and irritation. I stumbled upon a hack that appears to fix it without even having to use the domain mapping plugin, but I'm not sure of the downsides of it yet, if any.
I changed one line in wp-config first:
then after I set up the sites (I'm required to type them in as the sub-domain without the .com), I go back into Network Admin > Sites and change the Domain field to the .com version... everything works hunky-dory. Everybody can log into admin from their sites and the URL never shows improperly. I never installed the domain mapping plugin. One thing I've noticed is if I'm super-admin, I still have to log into each site as the super admin, which is fine with me.
Can anyone tell me what the downsides of doing it this way are? I'm still running on a test install.