Here is a good blog post that covers how to optimize performance: http://weblogs.asp.net/scottgu/archive/2006/09/22/Tip_2F00_Trick_3A00_-Optimizing-ASP.NET-2.0-Web-Project-Build-Performance-with-VS-2005.aspx

I suspect you might be running into the dueling references issue I mention in the article.

Hope this helps,

Scott