I just fixed this problem on my rMBP without AutoCAD, and I hope what I did will be useful to some of you.
First the fix, then some details:
-- Shut down all of your apps, except Finder (which you can't shut down and don't need to.)
-- Wait a minute or two to allow your OS to do some housecleaning. If you shut down your machine right away, you'll preempt some of the housecleaning, and you'll still have the problem when you restart.
-- Shut down your Mac (don't just restart; do a full shutdown so it will be less likely to save you time by doing only a partial cleanup)
-- Wait thirty seconds or so for everything to fade from RAM (probably unnecessary, but if you don't have to do this for a lot of machines, it's not much of a burden)
-- Restart, and I hope your problem will be gone
Some details that you can skip unless you are interested:
-- I had made some adjustments in the System Preferences > Accessibility > Trackpad > Scrolling Speed to increase scrolling speed. I didn't like the jerkiness of the faster scroll, so I set it back to the original speed. I didn't notice until sometime later that all my apps now had jerky scrolling. Maybe this adjustment caused the problem. Maybe it was my experiments with drag settings. Maybe washing my car makes it rain.
-- I did a restart and still had the problem.
-- I shut down all apps except Finder and did a full shutdown. I waited and restarted. I still had the problem. And then Firefox and Terminal started up with the windows from the last session. Strange. I had quit those apps (cmd-q) before shutting down, but here they were starting themselves. It seems as though the system thought they were still running when it shut down and restored them on startup. Hmm. I wonder what else it restored for me.
-- I shut down all apps and waited a couple of minutes, giving OS X plenty of time to straighten up the place and take care of those low priority chores it had been meaning to get around to. Then I shut down, waited, restarted, and Firefox and Terminal didn't autostart. Finder did autostart, of course, and when I tried scrolling a very full directory in Finder, it was back to smooth scrolling. I restarted my other apps and scrolling remained smooth. Problem solved.
-- There are probably several things that can hobble the graphics system this way, but I hope that this procedure will clean up some of them for anyone who reads this (and maybe suggest an idea or two to Apple engineers....)