Prior to getting my cpl here in MI, I had endless issues with NICS. Initially all my transactions got "canceled" after the 3 day delay. They made me file an appeal. They ignored the law and provided no reason why my transfers were getting delayed and then canceled. I finally got an official response (registered letter) saying there was no problem with my background check and providing me a UPIN number. Went back to the FFL. No change. Delayed, canceled. After 3 months of going round in circles, my FFL got mad and called and spoke to a supervisor. The lady said that there was no reason why my transfers were not approved and she approved the 2 transfers I had been waiting on immediately.
That suggests that (legal or not) the FBI agents sometimes use some personal discretion (or bias) in deciding whether to approve/deny or cancel.
After I got my CPL, that was the end of the problem. I also had no issues with my background check for my CPL, no any that our company legal department ran on me, nor when I applied for my green card. So go figure.... But I assure you, if I go to any of the big stores (Cabelas or the like) who have a POLICY of running a background check regardless of whether you have a CPL, then even today I have the same circus.
It is possible that this systematic issue is more prevalent with FFL's who call in the transfer, as opposed to those who use the online system. I just have not met an FFL yet who is using the online system.