I've not been able to reproduce this issue -- could you post more information about how you had your integrated instance set up (specifically concerning avatars) and how you executed your import (specifically the options you set.)
If you want to verify your two avatar per user theory, you could check your database (the jiveavataruser table)
Sorry. I actually figured this out last night... It appears something must have been stored in cache while I was mucking around with different DBs.
Once I started brand new, this and a few other issues went away.