oh and by the way, all Microsoft Servers now come with a rewrite url available during install (trust me, it has everything to do with WordPress, check their site)
If you are using IIS 7 on godaddy if is it a dedicated or virtual server?
Godaddy will e of no help unless you have purchased some sort of support contract with them (I was with godaddy and left)
Anyway, make certain the rewrite is imported and applied to the proper web configured on your server
I have three copies of MU running and to be honest with you, if you do not follow the above statement you will get some really strange results (funny actually).. wordpress will just randomly decide (seriously on the fly) which index.php it wants to follow if you don't load the rewrite into the server config... works ok on a single configuration however, you will or can run into permission problems... next question, Intel CPU or Athlon?