Apparently I'm having a similar problem. So I append myself in here.
My intention was to redirect a subdomain.com to its brother subdomain.org. So I parked the .com and setup a redirection via cpanel (Hostgator) to the .org.
Somehow something went wrong, and even if the subdomain.org is working fine, the primary site is broken. When I try to open a post, I'm redirected to subdomain.com - which is quite weird.
So, since even the (otherwise excellent) Hostgator support couldn't figure it out how to solve it, I'm rebuilding the whole network (not big deal). But I would really like to ask two things, before to proceed.
1. Is the WordPress MU Domain Mapping plugin strictly necessary? I've read that with WordPress 3.1 is superfluous.
2. What is the best practice for having a subdoman.com redirect to its counterpart subdomain.org? Setting up a redirect via cpanel, or mapping the two domains to the same subsite and then mapping one of the two as primary?
Thanks in advance, regards,