This sounds like a problem with the web application project. Are you using that for the project type? If that's the case then here's what's going on:
You compile the application in the IDE. This includes all the code files in the App_Code directory because they are included in the project list of code files. Then you run your application. .NET 2.0 automagically compiles everything in the App_Code directory when you start running your web app. This then results in 2 assemblies, one for the explicitly compiled application (Jennison.Affirm2.BLL) and one for the dynamically compiled code in the App_Code directory.
You need to move all the code files out of that directory so there isn't anything to dynamically compile.
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Peter