I decided to replace the hard disk in my Dell Optiplex 755 with a larger model (500GB). Migrating Ubuntu was trivial; Windows Vista was not. Clonezilla did its best but I ended up running into all sorts of Windows BCD corruption issues. Most of the various repair tools on the Windows DVD failed with incredibly non-descriptive error messages.
After giving up I quickly discovered that Windows would refuse to even install, citing Windows is unable to find a system volume that meets its criteria for installing. This was even after zeroising the first few GB of the disk with dd. WTF Microsoft?
Even a BIOS update didn’t do the trick. (hint to Dell, et al.: DOS is dead. Please give us a modern, OS independent BIOS update mechanism)
It turns out that two things seemed to have an affect on this: my HP Photosmart printer with its built-in card reader and floppy drive setting in the BIOS. Disconnecting the printer and setting the floppy drive mode from USB (default if there is no internal floppy drive) to None cured the problem.
By this stage I had wasted enough hours so didn’t even bother trying to see if the clone would work this time around.
Of course all along Ubuntu behaves just perfectly.