Save for reinstalling, what else can I try?
Considering my girlfriend is a Windows user, could it be that this is a setting that's available on the Windows client but not on the Linux one, and somehow got transferred?) (I remember there was a similar Skype setting somewhere whenever I've used it on Windows. Checking for a relevant setting in Skype itself - couldn't find anything of the sort.
My girlfriend logged into her Skype account from my Xubuntu 12.10 netbook, and ever since then Skype starts automatically every time I boot.