When I converted from CS 2.0 to CS 2.1 I only ran the CS 2.1 upgrade SQL script and when I went to run the site I got an exception regarding a TimeZone stored procedure parameter.  What it looks likes it is I was still using the older membership stuff in CS 2.0 and I hadn't upgraded to the ASP.NET 2.0 membership stuff.  So I ran the second CS 2.1 upgrade script which does something to upgrade to use ASP.NET 2.0 membership stuff and all has worked fine since then.

 

So not sure I had the same problem as you but seems similiar.