I am having a similar problem as described here: stackoverflow.com/questions/364637/asp-net-mvc-on-godaddy-not-working-not-primary-domain-deployment
I have multiple domains pointing to different folders. Each folder is set as an application root in IIS7 on GoDaddy's shared hosting. These folders are [ContentRoot]/websites/folder1, [ContentRoot]/websites/folder2, etc. Domain1 points to folder1, domain2 to folder2, and so on. Thus my understanding is www.domain1.com should grab the mvc app at /websites/folder1. And it does. However, the problem is all links using Html.ActionLink insert the full path. For example, Html.ActionLink("Some Link", "MyAction", "MyController") produces a link to www.domain1.com/websites/folder1/MyController/MyAction instead of www.domain1.com/MyController/MyAction. Interestingly, both URLs load the appropriate page.
I'm unsure whether this is a problem specific to GoDaddy or all shared hosting. I've been able to avoid this issue using IIS6 in a dedicated environment.
Thanks Eric