facing particle alpha opacity weird problem

Hi all, 
I am trying to make a short animation of flames using facing particles with an
opacity map and blobmesh with an opacity map, and for both those elements, the
alpha seems to have been calculated incorrectly. The squares of the facing
particles are still visible on the background though the bits that should be
transparent are now black on render.

The mat used for the facing particles has face map applied so I don't think
that's the problem.

I am using scanline renderer with 
motion blur, both image and object for separate parts, with a video as an
environment map. Here is an included image if you want to see what I mean.
Thanks in advance for all help!