hi Pete.
Crikey that's nasty.
I'm certainly not in the PI expert camp, but that looks like (rotated) column defects in the sensor to me - my guess is that will probably come from the flats. Maybe you could check the process for making the masterflat - could there be bias, dark or pedestal in there where it should not be - or missing where it should be included?
FWIW, I found that there are quite few settings that have to be right or the master cal images can get screwed up - I ended up using the following to the letter and all went well:
http://www.pixinsight.com/tutorials/...mes/index.html good luck.