Thanks, Scott. Sorry to hear that you're struggling with this symptom too; it really is debilitating. I assume the software you're talking about is f.lux, right? I have that installed too and it really makes a difference.
I do get some balance issues if I drive too much, but I don't think it's related to the photophobia. Vertigo hasn't really been a problem for me.
I started a couple of threads awhile back on making your computer more accessible for photophobia:
http://neurotalk.psychcentral.com/thread163832.html
http://neurotalk.psychcentral.com/thread166767.html
Here is another simple thing you can do that I didn't mention in those threads. Right click on your desktop screen and go to 'personalize'. Then go to 'windows color and appearance.' Try 'high contrast black' and see if it helps. You can also go in and individualize the color scheme from there, but I can't remember how and it can take a long time to get them balanced right.
Anyway, I hope you are able to see some improvement soon. Congrats on hanging in there with this condition and this symptom.
Pete