Most of the "Auto" Effects suffer from what you describe. They really only work so long as everything, the exposure, the lighting, everything, is uniform for the whole Clip.
Most use one of the Color Correction Effects, and not Auto Color, Auto Levels, etc.
About the only way to get the Auto Color to function, when the Clip is not uniform, is to Razor the Clip, when there are change in lighting, or exposure, but that is tedious.
Thank you Bill.
I just need a quick way to correct white balance differences and the auto color did it very well.
Three-way colour corrector maybe?
For White Balance correction, I like the Fast Color Corrector. Less power than 3-Way, but with fewer parameters, it IS fast, good and pretty simple. Explore that first, to see if it will get you what you need, and without the strobbing, that I see most of the time, in Auto Color.