Hah, thanks for finding that. Yeah, the hand axe is id 0, so it looks like save/load doesn't know what to do with the rune. (Much like players... :) )
Yeah you're right it's useless but I use it for immersion: I don't like leaving stuff and treasures lying around unguarded in a room, with the rune at least I'm putting an alarm on them :)
I have a fix for this. It's not in a build yet but probably in a day or two.