I've heard about this problem happening. I think tweetiepooh could be on to something important here. I was reading more about Berkley DB here:
http://www.oracle.com/technology/documentation/berkeley-db/db/gsg_txn/C/index.html
There is a lot of bookkeeping to keep track of a transaction and if you are in a situation where say 2 hours of inserts are one transaction which in theory could be aborted with no change to the DB, there's a lot of overhead there! A commit would say, "I'm finished with this one". I am not a DB guru. But I'm also wondering if there aren't some options that circumvent some of the normal transaction rollback and journaling for the case of a single user doing the initial DB create from scratch? I don't know. Just wondering if this initial build is somehow handled differently than the "online use" of thing thing once built?

Update: I would leave ouput unbuffered until you get this working. But you should be aware that there is a significant performance penalty for that. In this case, we could be talking hours of difference! Get it working, then turn buffering back on and see what happens. Right now I am suspecting that tweetiepooh's idea of committing every 100 or whatever adds is gonna do something impressive.