Scott,

 

Yes, I see. I have no problem precompiling the whole application into one assembly.

 

Here are my steps:

 

1. Right -click on any of my web projects in the solution (In this example, I am using Personal Web Site Starter Kit) and add a Web Deployment Project.

2. This will prompt me for what I want to name the project and where to store its project file.
The web deployment project will then show up as part of my solution.

 

3. Double click on the WebSiteDeployment node (which is a short-cut for the same thing) to customize its properties.

 

4. The default option is to merge the entire web-site into a single assembly that you can name however you want.  This merges the output of all page/control compilation, app_code, and web-services into a single assembly (leaving one file to deploy). 

 

5. Click Batch Build.

Hope it helps.

If you still have problems, please let me know the steps to reproduce the problems.