First - important point: this bork never left my laptop; this is not a problem in the package I mentioned yesterday!
Can you spot the face-palm in the following (that installs the protobuf-net Custom Tool into Visual Studio 2008):
That will install just fine, and the Custom Tool will work. And then you uninstall it.... oh dear. It helps if you know that {FAE04EC1-301F-11D3-BF4B-00C04F79EFBC} is Visual Studio's nickname for "C#". Did you notice that innocent little "DeleteAtUninstall" flag? Somehow it get set to true (it certainly wasn't deliberate).
Oh well, perhaps I can get by without all the inbuilt tools! Or maybe I need to rebuild my crippled registry... Fortunately this only impacted my laptop before I spotted it (I do test things, honestly!).
Still - it could have been worse; a few levels higher up and I could have completely broken Visual Studio (or potentially windows, but I would hope that the operating system wouldn't let me do something truly stupid, such as deleting HKLM/Software).
The moral of this: when you are writing installers, double check both the install and the uninstall do exactly what you expect. No less, and (perhaps more importantly) no more.