All of the guard's equipped armor and weapons are vanilla, the horse is vanilla, and all of the guard's custom race meshes (head06, merged teeth, etc.) are in the correct location and working correctly. Using the console and clicking on the missing mesh marker returns the refid of the guard (and, depending on where you click on it, the horse). It appears to be some sort of invisible object which is equipped when the guard is mounted, but only on occasion. (I've tested the mod hundreds of times and this is the first time I've ever seen it.)
Any ideas?
Edit: Nevermind. It appears I forgot to delete a line from a dialogue result script which was adding a token to the guard using my old persuasion engine. I've since changed the engine but missed cleaning this one dialogue. I guess he decided he liked the token enough to wear it. :facepalm: