There's a thread here (http://ubuntuforums.org/showthread.php?p=12345696) and the user seems to having problems with getting uniform results with mouse cursor themes installed from elsewhere.
I think the default is DMZ White but just to check I changed to DMZ Black. Even after a couple of reboots not all apps take up DMZ Black. The ones that work for me are Audacity, Firefox, and LibreOffice. Several don't: these include Chrome, PCManFM, Leafpad, and Evince. Please note that I have not installed galternatives (as suggested in the link) but simply followed the instructions in Customize Look and Feel because that is possibly what people would do. Can someone please confirm what I'm seeing? My set-up is a standard Lubuntu 12.10 install, fully updated on a Dell 1545 laptop.
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