Putting --dir-name-depth 1 appears to work, if I use any higher number, I see all directories highlighted; e.g., gource -1280x720 --seconds-per-day 0.001 --hide filenames,progress --dir-name-depth 2 --highlight-dirs --highlight-colour FF00FF -r 25 -o - | avconv -r 25 -f image2pipe -vcodec ppm -i - -pre libvpx-720p -b 5000K -an -y test.webm

This can be reproduced with the repo https://github.com/trilinos/trilinos.

Ah, never mind, it does seem to work now. Feeld free to close.