I have seen this also few times with skype and gtalk. It gets fixed if I disable skype and gtalk accounts and then activate them again. Some times green icon is also shown when I have already went offline for all IM accounts. I think that this is definitely bug in N900 and not with skype or gtalk service.

I don't have any details why this happens so I haven't yet filled a bug for this in bugs.maemo.org but maybe this should be filled anyway so that all information on this issues is gathered in one place. Bug https://bugs.maemo.org/show_bug.cgi?id=8475 might be related to this problem.