I did a considerable amount of software engineer recruiting during my career. I only called the references at an advanced stage, after an interview. It seems to me that calling references before an interview would take too much of their time (since if everyone did this they would be called very often) and too much of my time (since I think their input would rarely disqualify a candidate at this point). The interview played the most important role in my final decision, but when a reference mentioned something negative which resonated with something that concerned me after the interview, this was often a reason to reject.