I've been ignoring this for a while but just added a new domain and decided it should be fixed. First, I'm sure it used to work, really.
My multi-site has been running perfect since I carefully installed it and first configured it. I used the domain mapping and sunrise as directed, and made the redirect with wildcards pointed to my base (WordPress root) directory. It is set to be subdomain.domain.net I can whip together a site in nothing flat, all the themes, plugins, and media works. It is a bit bothersome editing CSS and such from the root account, but it only needs done once so I can live with it. I get everything beautiful and attach a domain name to the site I'm using (not the root - the sub-site or whatever it is called) and it looks beautiful.
What, you say, is the problem? I can't edit the darn thing. It refuses to recognize the admin/password it has all along and seems to have problems recognizing anyone. I do have the signup turned off, perhaps I need to turn it on so I can make a user with the domain name. I can't sneak in from the back as it puts me on the domain instead of keeping the sitename.maindomain.net syntax. I tried turning off primary. That gets me into the site, but the domain quits working.
I'm lost, I've been futzing with this for a few months then get tired and leave it. I'm sure it used to work, but maybe none at all.