I am farily confident that a 5 minute drive to work would not lead to dead batteries as there are many people who drive a short distance to work and don't experience this problem.
I would think this may have something to do with the new alternator / voltage regulator. Have you had it tested? From your note it looks as though the alternator is putting out what it should.
How dead was the battery in the first place? If a battery gets really dead it will not take a meaningfull charge again, someone has told me something about reversing polarity?
Did you install a new battery with the new alternator??
Hope this helps,