Thanks for all the responses. The violation I committed was a federal offense. So maybe this is why my passport was flagged. I know it was fagged because they told me it was. The process of the extra search was only on the bags. I was with my kids and wife at the time. It only took roughly 15 mintues and they let me proceed. I know it is not a huge deal as far as time is concerned. I may have to just put up with it. I am hoping to find out if other people have the same problem when scanning passports. I am hoping this does not happen every time I re-enter.
I know Canada when scanning passorts will deny you entry unless you get a rehabiliation approved which takes months. This is even if you have a DUI. Once you get approved you never have to worry about entering again unless you violate the law. So passports I believe do show every thing about your background.
Thanks again!!