I basically have the same issue as this question: Embed multiple icons in WPF EXE
My .NET 2.0 WinForms application currently has this when you click \"Change Icon\"
The article mentioned by ChrisF will also wipe out your assembly version information. Once you follow that guide you might want to try using the post-build method described here http://blogs.msdn.com/b/cheller/archive/2006/08/24/718757.aspx to embed the manifest.
EDIT:
It is "Method #2 - The "Generic" Approach (using mt.exe)"