I have been most fortunate to have a brick mason who works on my house from time to time and takes the MOST incredible pride in the job he does. Of course, he can only work when he's sober, so there's a tradeoff for everything, right?
It's too bad that there are so many craftsmen out there who should know better -- and either don't know or don't care (and some of them come highly recommended by people who, obviously, have just not yet experienced the problems these guys have left behind).
Over the past 20 years I have made myself very unpopular with a couple of guys who thought they'd sell me one thing and actually do something else. They seemed to think that what I didn't see wouldn't hurt them! Man, you've got to be there for every moment of every day of the job, and take nothing for granted. It's sad, really.
Best of luck on getting this flashing problem remedied, because I'm sure you don't need many more seasons of moisture before you start seeing the rot and mildew it creates destroying other areas. Keep us on posted on your progress!