It turns out that this crash is the result of a bug in the Wow64 layer of Windows x64 (XP/2003 – it has been fixed in Vista x64) and only manifests itself when another app globally hooks all Windows messages.
We are currently working with the Windows servicing folks to get a hotfix produced.
Updated 13 Feb:
Deep in the comments to the aforementioned request there is information about how to obtain hotfix:
If you are experiencing this issue you will need to contact Microsoft Customer
Service & Support (http://support.microsoft.com) and ask for the Windows
Hotfix with ID 947841. If you have any difficulty in obtaining the patch
ask the CSS representative to contact me (Sean Laberee).
I am also pleased to announce that we have created a workaround in VS 2008 SP1 which eliminates this problem and the need for the patch. That workaround is queued for checkin to our build process and will be available in the Beta of the service pack.
A quick update on the windows patch. I've confirmed with our support team that if you call in for this hotfix you will not be charged. They will set up a "Hot Fix" case for you. I've also received a report that there was some confusion as to whether this fix is for Win2003 or XP. I've confirmed that this fix does in fact apply to both releases.