That's a tough one...
I would say, from my experience, working in corporate security (Def. Contractors), that the mishandling of classified materials is just about as routine as the other stuff.
The government/governing agencies are often referred to as User-Agencies and they set the rules/regulations for the handling of materials and pretty much every aspect in regard to how the project/program is handled and carried out. The contracting agency is required to then follow those guidelines... However, if a member of the user-agency departs from the guidelines for whatever reason, it puts the contracting agency in a poor position... if you make "problems", you could potentially lose your contract. Make sense?
So, IOW... the user-agencies frequently break their own rules as it suits their immediate needs. I've personally witnessed this myself on countless occasions. Senators, VPs, Congressmen, senior staff, foreign representatives, and "key-players" in a program frequently are deferred to just because that's the nature of "power".
As for the transmission (electronic or otherwise), transportation/delivery, "couriers"... I think that the general public would be horrified at how lax protocol can be. Just as a "for-instance", when Clinton first became Pres., they instituted most, if not all, security clearance paperwork to be done online, and over the standard internet... not a secure server mind you. And that paperwork includes the very personal and private (sometimes classified) information of the persons submitting for a needed clearance.