I have indeed been able to confirm that this is a bug with rebuild_sprites.
This problem won't be apparent on all servers, which explains its sporadic nature and why it was hard for us to reproduce it.
This problem will only crop up if the server owner had previously rebuild sprites through WHM's Live Branding Editor. That particular situation presents this problem.
The problem is then that /usr/local/cpanel/bin/rebuild_sprites never rebuilds sprites found at /var/cpanel/cpanelbranding/
/var/cpanel/cpanelbranding/ is where WHM's Live Editor branding/sprites get placed.
I've filed a case on this bug for you now.
I wouldn't have an ETA for you on when this will be fixed, but it will be posted to http://go.cpanel.net/changelog
once it's been resolved.
In the interim, the work around (which I've already enacted on this server) is to:
 Go to WHM -> Branding. Select "Live Editor" for the affected theme.
 Go to "Edit this Style" for the affected style
 Go to "Edit Icons"
 Click "Generate Sprites"
This forces a regeneration of those sprite files that are otherwise being erroneously skipped by rebuild_sprites.