This is a known upstream limitation: hardware cursor is not affected by
redshift (at least with randr method, the default).
It is actually stated on the official website:
http://jonls.dk/redshift/
(search for "Known bugs and limitations")
A workaround would be to use software cursor, here is what I have to add
to the "Device" section of my xorg.conf to achieve this ('radeon' driver):
Option "SWCursor" "on"
But a real fix would be nice, seeing as some applications do not behave
as intended with software cursor enabled.
