I am these days working on a couple of articles about toolwindows. As you know, the package wizard has an option to create a toolwindow for you that creates a lot of stuff with guids, ids, attributes and so on. One thing that you notice when you learn about packages with commands is that there are duplicated declared Guids for the package guid and command set guid in the .vsct file (<symbols> section, guidVSPackagePkg / guidVSPackageCmdSet guid symbols) and in the Guids.cs file (guidVSPackagePkgString / guidVSPackageCmdSetString constants). That duplication is unfortunate but required, because those two files are compiled by different tools (the .vsct file is compiled by the Vsct.exe tool of the VS SDK and the Guids.cs file is compiled by the C# compiler). However, when you create a package with a toolwindow, you get a third guid value duplicated, but that duplication is not required.
I have documented it in this article:
BUG: Toolwindow guid attribute value hardcoded in code generated by Visual Studio package wizard
and I have opened a bug report at Microsoft Connect:
VS SDK package with toolwindow: constant guid not used in code, hard-coded guid instead
To prevent the problem in the future packages that you create with toolwindows, you can fix the templates by yourself as explained in my article HOWTO: Changing the source code of Visual Studio Package project templates.
And since I have verified that this problem exists in the templates of the package wizard since VS 2005, chances are that if your package uses toolwindows it has the duplicated guid value if you haven’t noticed it.