The second background check is probably to cover the period between applying for the permit and when you actually receive the pistol.
When I lived in Florida, I filled out the 4473 and payed for my pistol but didn't get a background check until the 3 day waiting period was over. the salesman said they did it that way so the background check would cover your past up to the time I actually received the pistol.
Now I live in Massachusetts and have a lot of prejudice against gun owners to put up with.
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