One way to tell if you're clipping blacks (or whites for that matter) regardless of your monitor calibration is to look at the RGB histogram...most processing software has this. Ideally, the peak is away from either side (left or right) and there's not an accumulation of pixels at either end.
This could of course be natural in your data...in which case, I'd suggest exposing for longer and seeing how the histogram moves. I've not used a CCD so I could have it all wrong
I only use a little DSLR though.