Could be that they view your advanced degree as a negative. They will spend a lot of $$ training you and if they consider you a risk to leave when you are weighed against an guy w/ an aviation bachelors /masters...well, who would you pick? I do think you'll eventually get there as the pool dwindles, but you're outside the norm for applicants and anything outside the norm right now is probably a risk to them. Keep plugging away and find some way to fly more frequently to show that you are committed to the profession.
To me, if I am on the interview team, I'd view your resume as someone who is sticking a line in the water but not committed to fishing. I might interview you if I had extra spots. You can't do anything about the PHD and it's a great accomplishment anyway, but bring your time in the last 12 months up to at leas the 300-500 range.