Comment 28 for bug 1304067

When your cursor is one size while hovering over the desktop, and another size while hovering over an application window, it's likely because the setting (Xcursor.size, an X resource) was set after your desktop environment was launched, like by a startup script or settings daemon. So some of the DE's windows (like panels or the desktop itself) will use the default cursor size setting which existed when they launched. A solution is to set Xcursor.size in a location which loads earlier than your DE settings daemon. An obvious place for this is ~/.Xresources.