My LGS says they got a handgun in from someone without FFL, and they wont transfer it because it came from non FFL.
I started dealing with a new private FFL holder last year. He said he sends a package of instructions to private sellers who will be sending him a gun, and sometimes they fail to do what he asks, which includes sending a copy of their state ID for recording purposes. That will hold things up as he has to request it again. It could have been something like that, otherwise it is just up to the particular FFL to determine their own policy.