I have a 2007 dodge Dakota with 112K miles. At 105K I had the front brake rotors and pads replaced. The rear brakes were fine. There was a problem with one of the rotors and I returned a week or two later and one, which was warped, was replaced. Ever since that second visit I have had an intermittent vibration from the vehicle. When I brake the whole truck vibrates. And by vibrating, I mean some pretty heavy shaking. It is not the steering wheel vibrating. I took this back to the mechanic where they were unable to find any issues with the brakes. Also, we could not (of course) re-create the issue while it was in the shop. I have not been able to find the pattern. It happens when I am braking at high speeds, but not every time. It also happens at lower speed, but again, not every time. Any suggestions?
those rotors are warped (still). i had that happen once and will never forget it. it is not subtle when it happens. did they take the rotors off the second time or just visually inspect it? it doesn’t have to be much to make it happen and you can’t really tell by just looking unless it’s really bad. bottom line, just bring it back again. eventually with enough complaining, they will want to make it (and you) go away 
“When I brake the whole truck vibrates.”
It sounds like the rear rotors might be warped this time.
Your mechanic should measure the rear rotor runout. If it is extreme, it might not be possible to machine them without going below the discard thickness
“we could not . . . re-create the issue while it was in the shop”
No, you have to apply the brakes at freeway speeds to experience the issue
That is why I test drive vehicles on the freeway BEFORE I pull them in the shop
I want to get a feel for the vehicle BEFORE I start on the service, oil change, etc.