As Geoff suggested, sounds like a problem with your master dark. Compare statistics (Statistics process) for a couple of your lights and your master dark. The median value in the lights should be more than in the darks. If it isn't, when you calibrate with the dark you'll end up with zero values where there isn't much signal in the lights.
If the darks are the problem then next you have to figure out why they don't match... You could also try setting a pedestal in ImageCalibration as a workaround.
Cheers,
Rick.