Well, I had been putting the lights.rad file in the same directory as vrad.exe. However, I took your suggestion and used the -lights parameter to load my custom lights.rad, and it processed it. Since it has no effect on the final compiled map, I'll just leave the other lights.rad alone and use the secondary file.
As for the sun flagged textures, I was using one and it didn't emit light until I added it to lights.rad, even though it was possible to see it in complete darkness until then, but then so were some of the non-sun-flagged lights, so who knows?
Thanks for all the help. Time to run around in my texture-illuminated cube.