I got it guys...follow below mentioned settings...
Use 'Chroma Key' to remove background & export as .mov file.

Export Movie Settings:

Compressor - Animation;
Color Depth - Millions+ of colors;

Keyframe and Rendering:
Tick 'Deinterlace Video Footage’

Before you try this, install flash 8 for latest codec/alpha channel support & QuickTime latest version.
instead of animation i have been using tga and not clicking the deinterlace (which i will try now). dont know what difference having the latest quicktime makes so i will check that out as well.

all the other settings the same but you have to play around with the chroma key settings (similarity, blend etc.) for the best results.

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