There is some pain and agony involved in the upgrade process. Any upgrade is typically painful in someway. However, this upgrade was particularly painful. Why? We had to make some changes to the UI due to Section 508 issues at the same time. As a result, the UpdatePanel was being use extensively. Everything was going along swimmingly, then boom. One of the new controls wouldn't display correctly. Thankfully, Peter Blum and I figured it out. The <head> tag has to have runat="server" attribute. .NET 1.1 apps that are upgraded don't have this setting.
BTW, Go BUY and USE Peter's controls. They are really good! Check out his site: http://www.peterblum.com/.