gource -1024x768 --stop-position 1.0 --highlight-all-users --hide-filenames --seconds-per-day 5 --output-framerate 60 --output-ppm-stream output.ppm
ffmpeg -y -r 60 -f image2pipe -vcodec ppm -i output.ppm -vcodec wmv1 -r 60 -qscale 0 out.wmv
The key was the image2pipe format which seems to extract all the frames from the ppm rather than treating it as an individual image.