Before I start, I'm assuming this is caused by poor ordering of the server aliases in httpd.conf and vhosts.conf ,, but could be wrong
History - working WPMU upgraded to 3.0 MS during site development (ongoing) then upgraded to 3.0.1 a few days ago. Currently main blog and child-blog for developing parent and child theme that will be used when the site goes live.
Under 2.9.2 with the wildcard subdomains set on server and in DNS, I know the mail servers and webmail mailboxes worked and were accessible, never checked them during the 3-4 weeks 3.0 was running, but after 3.0.1 I had cause to go check a test mail had been received after adding a plugin today (Sitewide Newsletters plugin).
None of the mailboxes were available - they all just returned http:500 or 404 errors. trying to browse direct to webmail.domain.com as per hosts help didn't yield the webmail login splash, it just dumped me back at site home with a message I was already logged in and sub-blog webmail did not exist.
Trying a dumbcluck back-end workaround like browsing to webmail.wp30domain.hostingaccountdomain.tld just dumps me at the search engine "page not found" default (as expected).
Have got the hosting techs looking into this but wanted to share it with everyone in case anyone else hits this issue - my suspicion is that the *.domain.tld in http.conf or vhosts.conf is too high in the list for the domain, and that it's knocking out the fixed-name subdomains for the mail servers - pop3.domain.tld, smtp.domain.tld and so on, because its just reading the wildcard and handing over to htaccess and thus WP, rather than resolving to the correct A records from DNS.
Anyone think it might be something different?