Tim, on the Q of dither, check this link out.
http://www.adass.org/adass/proceedings/adass99/O6-02/ That said, I would start sort of where Sanders said, closer to the basics, don't Calibrate, just convert your 14bit CR2 files to .fit files with the BatchFormat Conversion script . This procedure seems simple but it's full of pit falls.
First go to the Format Explorer tab, check the attached image for the settings.
Second click BatchFormatConversion under Scripts/batch processing changing the default settings see attached image.
Image Integrate some of your longer image sets, this is a starting point.
Next you can make a MasterBias form around 50 iso100_1/4000 subs with the Camera covered with aluminum foil to keep out the light, convert with BatchFormatConversion
read this,
http://pixinsight.com/forum/index.php?topic=2570.msg19019#msg19019work with the MasterBias first, try Calibrating some of your lights say 6 of the longer sets, see how the dark back ground level changes between unCal and Calibrated lights.
Then try to make a MasterDark work, and then a MasterFlat...
Cleon