That's really odd. Make sure it's using the new directory on the new drive. (check the block file timestamps in both). Did you try an older version of bitcoin-qt? If you really need it working on this particular computer and you don't want to reinstall windows, you could install linux in a virtual box as a kludge.
fresh install to a new dir on new disk. new directory on a new hdd for blockchain, wallet etc.... everything is running of of a new disk.
it's a bug.