If you have your website setup internally at development.website.com, test.website.com and externally atwww.website.com. Does the publickeytoken need to be different between the three websites?
I am using the same public key token for both internal interations of the website and the external and have not run into any problems. I had an issue with forms authentication - the cookie when they all had the same cookie name.
<compilation debug="true" targetFramework="4.0"><assemblies><add assembly="AjaxControlToolkit" /><add assembly="System.Data.Entity, Version=4.0.0.0, Culture=neutral, PublicKeyToken=23sdf2349s22" /></assemblies></compilation>