Kill only one pylon at a time, and only on the platform that you land on. We had range that would kill the pylons from a mile back, but that would make him bug from time to time. Our guild just killed Soa on hardmode and for the past few nights we have gone with the one pylon method and his orbs have not bugged since.
That's funny, we would have that issue when we killed them one at a time. We had our gunslinger take them out at range and we killed him the first time we did that. That was the first, and only, time the third pyramid actually scored a hit.