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...

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.