This has been answered in a separate question and resolved the problem for me. Be sure to vote up the original person’s answer.
ASP.Net error: “The type ‘foo’ exists in both “temp1.dll” and “temp2.dll”
Add the batch=”false” attribute to the “compilation” element of the web.config file.
This problem occurs because of the way in which ASP.NET 2.0 uses the application references and the folder structure of the application to compile the application. If the batch property of the element in the web.config file for the application is set to true, ASP.NET 2.0 compiles each folder in the application into a separate assembly.
http://www.sellsbrothers.com/news/showTopic.aspx?ixTopic=1995
http://support.microsoft.com/kb/919284