I think it is non-US citizens that don't normally get the *CLR* on the BP. I don't get it on my BP's in the US and the flights are always on an international ticket (mostly RTW).
Even before 9/11 my bags were often flagged for x-ray at check-in. Post 9/11 they have always been x-rayed at check-in (not a lot of flights to compare with though). Has never been a problem and only takes a few minutes, and the staff have always been polite en efficient about it.