Render to transparent issue

Hi,
Could someone please advise on this issue:
I have rendered off a set of PNG files with Alpha from 3DS Max with a view to creating a transparent background video.  When I import into AE the background is transparent (toggle transparency grid works).  I have also created a heat haze effect in the AE file using an adjustment layer and red/green particle layers (if you are familiar with the tutorial).
If I play in AE or scrub the timeslider the chequered background is there and the heat haze is there.
I used the following settings to render from AE:
Quick Time video
PNG Codec
RGB + Alpha
Millions of colours
Straight
The resulting QuickTime mov file has a black background and also shows the red particles layer from the heat haze (behind the main scene objects).
Q.  I am sort of guessing that it is the haze/particle layers that are producing the black background in the final video.  Is there some setting for the haze/particle layers somewhere that I am missing?  Or is there another reason?
I am not particularly experienced in AE so don't be afraid to state the obvious!
Many thanks,
T

I am having a similar issue, however the difference is I have a layer to replace the transparency in AE.  It works in the sequence and with RAM preview, however when I render to Animation with RGB Millions +, I get a black hole.
I am positive I am rendering without Alpha.
Thanks for any advice!
- Ryan

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