All was well you said. Well not quite.
The PC started to complain about Windows update not working, search not working, crypto32 not working and downloads using internet explorer not working.
A virus you say.
Not exactly. The new hard disks run a sector size of 4K rather than 512K, which effects a lot of default apps. In the end I had to install a newer version of the Intel Raid driver to make this all work. For an explanation see KB 982018