This is a very common situation. I have a very clean record aside from a couple of traffic tickets over 20 years. I am delayed every time I buy a new gun. It was explained to me that if you have a similar name with a not so nice guy you may be delayed until they make sure that you are not him. I have a friend who is a LEO and he ran my name and sure enough there is a guy in St. Paul with the same name and a record that goes on forever. I think I am pretty safe to assume that is the reason for the delay every time.
I am sure there are many other reasons too. It might make you feel a little better to know that this delay is never to long. A few times they have called me before I got home from the store to tell me I am good to go. I would not hurt to call and check it out often.
I think it is a small price to pay to make sure guns are being sold to the right people. I just blow it off now after many delays. You will have your gun soon and it will all be a distant memory. Good luck with the new gun!