gnome-screensaver warns if it sees Num Lock enabled.  ThinkPad laptops (and possibly others) have a setting (enabled by default) that makes Num Lock independent for internal and external keyboards.  This allows the use of Num Lock on common external keyboards with real numpads, while not enabling the overlay numpad on a laptop keyboard that prevents normal typing.  With this setting enabled, gnome-screensaver will warn about Num Lock if the external Num Lock is enabled, even when using the internal keyboard with no external keyboard attached.

At a minimum, gnome-screensaver should only warn about Num Lock for attached keyboards.  It would also help if gnome-screensaver said *which* keyboard had Num Lock enabled; that would help track down issues like this more quickly.

In an ideal world, gnome-screensaver (and other applications prompting for passwords) would have some huge database of keyboards that have overlay numpads, and only warn for those, but as far as I know no such database exists.