^^ Actually, they simply had an unresolved question, and wanted an answer. I can see where an arrest with no disposition "pro or con" would stimulate a question. Frankly, I am surprised the question was not raised much sooner in my history of (many prior) background checks. Once the question was answered BATFE issued the FFL without further correspondance.
So the takeaway is that BATFE uses more then the basic NICS check database. But... dunno what databse they use. The CCW applications and the security clearances I had been thru before were done thru the FBI and were never a problem. Just dunno.