This post has been very educational... I am happy you finally got it sorted out. As an Oregon based FFL, I know these things happen on occasion, and often make little or no sense. Believe me...we are just as frustrated as you are. I have a friend who is currently going through a similar circumstance, and will also have to go through an expungement in order to straighten it out. The moral of the story is...
If you have had ANY misdemeanor in-custody or criminal summons contact with law enforcement (No matter how long ago), be proactive in expunging the record as soon as possible. You never know when or where it will surface and bite you.