Hi Andrew,
I think that when using auto ISO you'll always get flicker. You could try using a variable ND filter and adjust it as the sun rises (or sets) but you'll probably still get flicker.
I think you'll need to fix it in post. We've used deflicker plugins for Nuke, After FX etc at work but if you don't already have a compositing package that could be quite an expensive route.
A bit of googleing led me to this:
http://www.granitebaysoftware.com/pr...roductgbd.aspx - It is standalone for windows and it has a trial so could be the way to go.
This also looked interesting:
http://lrtimelapse.com/ - a plugin for lightroom.
Oh and you have of course set a manual white balance? I've forgotten that on a couple of occasions and it can add a nasty flicker.
Good luck!