Leonard, are we to understand from your post that you did not file via the US eApis system? How did you receive landing rights authority (which is not customs clearance but merely permission to arrive). If you relied on an FBO to do that for you then that, with all due respect, was somewhat foolhardy.
I don't have the exact date at hand, I'm in a hotel, but I believe it was May 2009 that eApis use became mandatory for arrival to the US. It can take 3 or 4 days to get set up in the system initially. Unfortunately, as has been said by many people in many a circumstance, ignorance of the law is not a defence.
As a flight crew member, I have been flying into the US at least once a week for the last 35 years or so. I always follow-up any documented procedure with a phone call to the port of entry to ensure everything they require is in place. Often times various entry points have some "local" additional procedure that if complied with will make your entry so much smoother. KBOS springs to mind.
Customs inspectors generally wield a great amount of authority and discretion and aren't typically shy about using it. You would be well advised next time to educate yourself as to proper procedure.