Not a contradiction. I don't believe in omniscient or all powerful
devices that function like literal deus ex machinas and heal everybody all
the time. It was stated *plainly and clearly* that the device was used
in healing terminally ill patients. They cannot undo physical damage from
gunshots (the regen packs and other devices were used to heal Garibaldi's
wound, and the alien device was used to raise his life energy level enough
to bring him out of the coma). The emperor suffered a massive attack that
destroyed parts of his heart. Can't be fixed by this device.

jms