My experience has actually improved substantially in the last 10 years or so, and most of the government systems I encounter these days actually handle it properly (as well as handling suffix properly too). That said, I've somewhat recently started having trouble checking in for flights again -- I flew last month and it took the ticketing agent >20 minutes to find my reservation on both the outbound and return flights, even despite my providing the 'confirmation code' / itinerary email (we were checking bags & flying with infants, else I'd have done online check-in).
It can be really frustrating -- though I'm hopeful it will continue improving and hopefully be a smoother experience by the time my kids are adults.