Mostly, questions were related to the operational challenges, day to day activities, and projects.
Director was mostly concerned if I could fit the company's culture. I was asked if I could deal with the situation where I have "$5000 coffee machine on my right hand side and a fridge filled with beer on the left hand side" (they really have both at the office). I guess the fact that I am not drinking beer and was not showing enough appreciation to the $5000 coffee machine automatically disqualified me from the process :-)
I was asked a bunch of inappropriate questions related to my ability to adjust to the unique culture of athenahealth.
At the end I am happy I am not with the company!
I regret I went so far in the interview process; very time consuming.