Comment 29 for bug 551965

Hi Scar,

The "problem"/feature made it into the release installer, but it has been noted in the release notes. Consider yourself lucky to be able to change it to IDE mode and clean the partitions.
To confirm this is the problem you have described, try installing Ubuntu from a preseed file containing the following option:
d-i partman/alignment select cylinder

This should cause the setup to align partitions to the cylinder instead of the optimal behaviour. If everything works then you have encountered this particular bug.