After reading all of this, I am thinking they may ask certain questions based on the ports visited. I know I said this before, but when coming back from Bahamas they sometimes don't ask anything, they just collect the paper.
But when I took a post cruise flight back to St.Thomas from San Juan for a few days extra and went through it was like the 3rd degree. And mind you I had came from PR
and leaving the Virgin Islands both US territories flying back to the US. It was 3 weeks after 911 though.
And they ask on the paper which countries you visited, so is why I think it might have something to do with it.
Sorry for the long winded post, just trying to figure it out myself.