Hey, I was on the wrong track here.
First off - sorting as not needed as we're not using the depth buffer for the particles (but rendering an opacity map to allow us to composite instead.
Because the depth buffer is off we don't have the issue of draw order changing blending results
My problem was actually that I was culling particles based on particle position and view frustum. this meant that whenever a particle centre position was off screen, the whole particle would disappear. I was confusing this with the z order of the particles changing.