Same problem not skipping Elites, had it in the previous versions of Trinity as well (at least since patch 2.0).
Using the exact same profile as Biotin. My build is only a little different tho:
Barbarian - Game Guide - Diablo III
(Latest version of DB - Stable.)
And the weird thing is; sometimes it does seem to skip elites, and other times it's just like I never checked the checkbox
As I said before, I had the feeling it 'sometimes' skips elites and it 'sometimes' doesn't. I did a bit more testing, and I have the feeling it has something to do with restarting the bot:
If I start up DB and just press 'Start', everything seems to work (I have 'Skip Elites' checked upfront). Even after a game or 10, it still goes the way it should. Now if I would press 'Stop' and later on press 'Start' again, I have the feeling it forgets I had 'Skip Elites' checked. This doesn't seems to be the case when I only use the 'Pause' button.
Now I may be way off here ofcourse, but who knows this info might help you find the solution to the problem.
@Biotin, could you maybe try the same to see if it works for you as well?
Something I also noticed:
At a certain point, the profile will start, take the portal to crypts and exit the game again without doing the run itself. Now this doesnt occur very much tho. But if it does, it will do it for a few runs in a row.
Now this only seems to happen when a new update of DB is available, and the client isn't updated yet. For each time I noticed, when I shut down the client to restart it, an update popped up. Now this might be pure random as well, but I just wanted to let you guys know, just in case.