This is what happens when people fail to have records expunged or sealed and follow up with destruction of finger print cards after cases are dismissed.  Although sealing and expunging records (depending on the state the manner is different and the law differs as well) can in most instances keep the records from view from most agencies, the records can still be seen by some governmental agencies.  I would speak with a criminal attorney in the area that you were arrested about expunging the record and what you can do the help with the Customs Issue. It may be the best way to have it taken care of once and for all. Good luck to you.