Sorry for the late reply.
When I looked at this earlier I couldn't come up with anything unifying those who got double credits. It just seeded random. I will take another look at it let you know what I find.
Inside credits_core.php I added some debugging. The 'commit' function ran this mysql insert:
The 2 items inserted are identical except from the timestamp, thus resulting in double Welcome's being credited.
I'm posting this screenshot for Annomate Dave. It's an admin shot showing how some of our members get credited twice for the Welcome activity. Seems like the second credit occurs seconds after the first.