this is kind of a normal thing, it depends on what reference frame you use, how bright your flats are between channels, etc.
you need to always, no matter what, do BackgroundNeutralization and ColorCalibration to your light masters. this (or the one-stop shopping of PhotometricColorCalibration) will fix the colors, every time.
make sure when setting the background threshold in BN that you set it high enough to capture the brightest background channel, or it won't do anything. look on the console to make sure that it actually applied a scaling factor to each channel.
rob