The only real issue I have seen is formatting issues with the header.ascx and footer.ascx . This is due to the fact that the 1.1 version doesn't have master pages. Thus when you try to convert to 2.0 It doesn't like it when you have your HTML tags split up between pages. What I mean is that in 1.1 the <HTML><Header><BODY> tags are in the Header, the </BODY></HEADER></HTML> tags are in the footer, and the page that contained the header and footer user controls between doesn't have these tags. Sure, when the page is compiled and sent to the browser it would have all the tags in the right place, but .net 2.0 doesn't like it. In 2.0 you use Master pages to do this, so when you try to do it the old way in 2.0, it causes problems. I believe it is most noticeable on the register or login pages. It wasn't something that I was able to fix in a short period of time, so I have not finished yet.
-Dycacian