In my solution when I click to launch the BOM, I immediately get this error:

NullReferenceException
  Object reference not set to an instance of an object.

Source     : MicroFour StrataFrame AddIns

Stack Trace:
   at MicroFour.StrataFrame.AddIns.PartialClassBuilderDialog.SearchWithinFolder(Project Folder)

I can't figure it out...

Can you post a screen shot of your SolutionExplorer.  I'll bet you've got some sort of special solution folder in your solution that we're not expecting.  Though we have null tests all over that method, so I'm not sure which one is being missed...

The only thing that has changed is that I added a Web Deployment Project to my solution.

OK, let me try adding a web deployment project and see if some of the DTE support is not available on it.

I don't have a "Web Deployment Project" template anywhere on my machine, but I have a "Web Setup Project" under the Other Project Types -> Setup and Deployment.  Adding one of those does not cause a problem with the BOMapper.  Could you send me a sample solution or a snapshot of your Solution Explorer so I can recreate it?

Here is a link to the Web Deployment Project template download page at Microsoft:

http://msdn2.microsoft.com/en-us/asp.net/Aa336619.aspx

Yep, that reproduced it in a hurry.  Looks like that project type's object model is an empty Project object with a null ProjectItems collection... not just an empty collection, but a null collection.  Man, I wisth MS would be consistent with the ways they implement the interfaces on their DTE object model...

Anyway, here's the DLLs for the fix.  Just put them in the common files folder and then the GAC and restart VS.