It also affects me, the same way as described, only with *.desktop files. Ubuntu 12.10 64-bits. Also using Gnome Shell from PPA, Nautilus 3.6.3.
I recall that the first time this happened I changed the size of the icon in my desktop and this border disappeared, but this is not working now. ** Attachment added: "Captura de tela de 2012-12-02 16:46:20.png" https://bugs.launchpad.net/ubuntu/+source/nautilus/+bug/1085320/+attachment/3449949/+files/Captura%20de%20tela%20de%202012-12-02%2016%3A46%3A20.png -- You received this bug notification because you are a member of Desktop Packages, which is subscribed to nautilus in Ubuntu. https://bugs.launchpad.net/bugs/1085320 Title: White borders around *.desktop files on the desktop Status in “nautilus” package in Ubuntu: Confirmed Bug description: Ubuntu 13.04, Nautilus 1:3.6.3-0ubuntu2 Desktop launcher files are drawn on the desktop with a heavy white border and very thin border in Home Folder. This only happens with *.desktop files. Links, folders, and files display normally. To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/nautilus/+bug/1085320/+subscriptions -- Mailing list: https://launchpad.net/~desktop-packages Post to : desktop-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~desktop-packages More help : https://help.launchpad.net/ListHelp