I successfully installed Multisite on my main domain two days ago.
I am using my main domain for the network as well as a blog and both are working great.
I added a second subdomain (wild card added during network installation) and mapped it using the domain mapping plugin.
The subdomain works, I can access the dashboard, the parked domain works.
The default permalinks work. (/?p=123)
What is not working is my custom permalink of (/%category%/%postname%/) that is not working.
I use shared hosting from HostGator and the tech suggests that I use the permalink that works (the default).
Yuck! Ugly and terrible for seo.
Oh yeah, most of the plugins I am using are supposed to work with multisite. I deactivated all of them (except the domain mapping plugin) and was unable to get the custom permalinks to work.