there is an easy fix to this. just turn off “pass custom alpha channel” in custom entries option of the rendersettings. in some cases you should only overlapping fluids container in one render layer.
rendering Fluids as dense Particle cloud is common practice. the Krakatoa plus for maya or 3dmax is based on this concept. even without this plugin, you render the particles as point in maya hardware render or as clouds in maya software renderer or mental ray. the advantance: fast render times and most important –> motion blur !
on the right side i switched to software clouds mode and used radiusPP over lifetime
a while ago, i did some tests for calculating motion vector from maya fluids and override the fluids color to render a motion vector pass in mental ray. i wrote python script and it work very well but the motion vector math in python took 15-40 minutes pre re. on positiv side it works with all kind of renderer, even the old school hardware render buffer.