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If you install Windows while the hdd is in IDE mode, you need to install AHCI drivers to Windows before switching the SATA mode in BIOS, or Windows will BSOD on re-entry due to not having the correct driver to mount the OS partition.
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This is how I originally set up my system. I installed Windows in the IDE mode and then installed the AHCI drivers after (then I had to use a Registry 'hack' to get it all running properly).
As to what the Live CD did to my BIOS, I am honestly not sure but it is a bug and others that run AHCI or RAID may get the same issue as I did so I just wanted to get this out as a fair warning to anyone wanting to try a Ubuntu Live CD.