Other users with experience in practical topics (I am a pure lab nerd these days) hopefully will chime in to provide more useful information, but in my opinion, color balancing should always be done just after preprocessing, while still in the linear phase, using appropriate tools such as BackgroundNeutralization and ColorCalibration, along with HistogramTransformation and others. Just let the raw data be acquired without modification by the preprocessing tools. If you use the BatchPreprocessing script to calibrate and align your data (strongly recommended) this happens by design. If you use the ImageCalibration tool manually, make sure you enter 'raw cfa' (without quotes) in the input format hints parameter.