John,
I've seen a lot of this in the field. Alan's right, the best time to archive a box is when the user isn't looking. At least for the big initial ingestion of their mail. I've also noticed that EV7.0sp1 does a much better job of not crushing a mailbox on archive run, even during it's inital ingestion. I do recommend upgrading if you can. It seems to be worth it.
micah