Morgan, a couple of things.
Firstly, I would never rely on Automatic White Balance, as that can change from shot to shot. When a texture is built, an image, or part thereof, is chosen for each area, so with non-fixed WB, you could end up with two adjoining areas being textured from images with different WB. I would always shoot at a fixed, known WB; that also means, if needed and the circumstances permit, I could go back and repeat or even infill.
Re the problem with an apparent shift in the whole textures colour: can you check if the shift is happening when the images are imported? i.e. if you import and then open one image in PhotoScan, before building anything, are the colours the same as in your RAW image?
Dave