I am setting up a multi-site implementation for a site and I am just about to wrap it up.
This bug is interesting, the situation follows:
1. User is logged in
2. User has created subdomain
3. User attempts to go to mysite.domain.com
4. Request results in 404
If anonymous user accesses mysite.domain.com, it works without issue.
wildcard domain is setup on host properly.
Permalinks are different from main to subdomain ~ which might be the difference.