Ok, after removing two of the hard drives and installing the system without RAID the problem still exists. As a test I installed the emacs23-nox package and watched 'iotop -ako' and with the exact same amount of data written to the disks Alpha has an IO usage of 60% for dpkg and ~35% for jbd2 where bravo has about 5% dpkg and ~1.75% jbd2. So it seems there is a massive overhead for Alpha to write the same amount of data to the disk at the same rate. I will be testing this theory more with rsync to see if the overhead ratio holds.
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