I have been trying to figure this out for hours and I think it is a bug.
I do not have much experience with WordPress but I have been working with other CMS for years.
Problem is as follows:
I'm using multisite (subdomain install = false) with domain mapping.
Main site works fine
Second site (no domain mapping) works fine when you go to http://maindomain.com/site2
Third site (domain mapping) works fine when you go http://anotherdomain.com/ but if you go to http://maindomain.com/site3 it redirects to http://anotherdomain.com/site3 (which produces a 404). I was expecting it to redirect just to http://anotherdomain.com/
I'm guessing (not sure as I have not tried it) that if if subdomain install = true it works fine as you're always requesting "/" and not "/site_xxx"
Am I doing something wrong or it is actually a bug? I have thought of several workarounds (rewrite rule, create a page call site3) but I think that are inconvenient...