I tried auto white balancing and it went a long way toward fixing the issues. I did have to manually reduce the brightness though. Is there a way to control the brightness adjustment in ppm_tiff_writer?

I'm also noticing that the red and blue channels appear very compressed in the output image relative to the green channel. I'm not sure what would cause that.

[edit] I set no_auto_bright = 1 and no_auto_scale = 1 and that seems to have helped. Not sure why one of those would have compressed one channel and not the others. I think I'll probably need to do some custom analysis of the negative to set the white balance and scale of the resulting image. Something about inverting the values seems to throw off the automatic processes.