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Are you using any of the channel calibration or alignment options? I've found they can mess around with the histograms and I leave them disabled and do the colour balance myself using levels.
Definitely look at the histogram of the source images. If they're too far to the left, should be able to stretch OK in post-processing. Essentially, when you're capturing the images you want the histogram to be clear of either end of the scale - too far to the left is underexposed, the right over exposed.
But also bear in mind that M42 is a tricky one to process because of the huge dynamic range, but it's easy to get data because it's bright.
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