I discovered the hard way that Microsoft’s sysprep tool (for configuring machine images) re-writes (at least some of the time) the boot.ini file, the file which tells the Windows initial bootloader which OSes are installed on which devices and partitions.
The new boot.ini contains the same OSes as the old one, but it specifies a different default, and a zero timeout for the user to choose what to boot.
I can imagine some reasons why sysprep might want to do this, based on speculating how I might deploy enterprise images.
Only the thing is, if I were going to re-write boot.ini, I would at least check to see which OS was currently running and maybe make that the default. As it is, sysprep made a different OS the default – it picked the “first” OS in the device tree even though that is not the OS I was trying to sysprep. This behavior seems more like a bug than a feature.
In any case, if this happens to you, there was no long-term damage done -- you can just reconfigure the boot.ini file by hand and restart.