These interrogrations of US Citizens of Pakitani origin are becoming fairly common. I know couple of co-workers (of Pakistani background) that went through the same.
As regards Continental Airlines, I have found their ticketing staff to be extremely rude and unhelpful. I stopped flying with Continental. I am not surprised they didn't try to help you.
Yeah, I really felt comfortable on American Airlines, the attendants really go out of their way to make you feel welcome... The only problem is once I get to the airport though:)
I will fill everyone in on my return trip in December.. Hopefully nothing will happen, but if it does at least I will have an interesting story to tell:)