Can't say I've ever seen this, sounds like something in the charging circuit is dead. Question is, is it in the charger or the remote. If you have access to another remote, will the charger work with it? Also, after you've charged it, is the battery really low, or is it just displaying the low bat icon? I.e. really a charging problem, or just a false indication?

As far as firmware goes, it might fix the problem if it's just a false indication, otherwise it seems like a long shot. However, a firmware update has fixed all kinds of strange behavior in the past, so it's worth a try.

I'd also try leaving the batteries out of the remote for 24 hours and see if that helps.