Guidance Packages are awesome, but they do have a way of driving me crazy sometimes.
They have a new version of the Guidance Automation Extensions, which is basically the runtime or framework that plugs in to VS.
The new version was updated to support VS 2005 and VS 2008. The documentation indicates that the installers for guidance packages are now supposed to prompt you for which version of VS to install into.
After searching and reading about 20 different articles, plus using Reflector on the GAX dlls, I finally figured out that you have to put code into your setup for the guidance package to tell it which version to install into. By default, it seems to go into VS 2005.
Here's the forum post that kind of helped:
You have to extend the custom actions so that they have "/Hive=9.0" in the string. This tells the GAX install engine to put it in VS 2008.
Painful, but in the end its still worth it.