It seems that support for MPEG-2 in After Effects is a "known issue" as the official Adobe support recommended I use a different source.
After serveral attempts at conversion with serveral different tools to several different formats, I have now found one that seems to work.
the wonderful ffmpeg is a command line tool that can convert from pretty much any video format to another.
For my camcorder and after effects, I have found that conversion to WMV2 seems to work best.
Anyone trying to reproduce this should try the following:
ffmpeg -i {input file} -vcodec wmv2 -vb 8900000 /
-acodec wmav2 -ab 384000 {output file}This should keep the video at the same quality (or close enough) as the original.
