What do you mean by your passport was flagged? Did they specifically reference your criminal record or was it just a unexplained secondary inspection which could have been for any number of reasons or even more likely, for no reason? In any case, I had.....shall we say... a very very very serious little indiscretion way back in 1991. It has never personally impacted my interaction with US Immigration or Customs in any way that I can detect. I'm quite certain the details are readily available to them if they go digging in their computer but I am also certain it is NOT flagged front and center to pop up on the first screen they see when they run my passport because it's the type of thing they would likely mention if they saw it and they never have brought it up, even in a few customs secondary inspections. Perhaps it would be different if the conviction was for something that could be construed as related to smuggling or something. Not sure. They can flag you for any reason, or for no reason but it is definitely not an automatic thing just for a criminal record.