Henrik Juel ,

 

I guest the problem is that your root app and the sub app use the same key for ASP.NET Forms authentication.

 

in web.config , you can see something like :

 

<authentication mode="Forms">
   <forms name="YourFormsAuthName" />
</authentication>

 

If your root site and sub site use same name , the sub site will get error because the root site send your sub site the invalid cookie.

 

So , please modify the sub site , and use another name.

 

--

If you want to keep the same name ,

      you need specify the machineKey for both site.

      Please check this for the machineKey : http://msdn.microsoft.com/en-us/library/ms998288.aspx

 

Regards,

Terry