Oh well I’ve just tried to process the stack of 2.2k images again (just the images) and the unexpected program state happened again, I tried to isolate the images just to check that I didn’t have any corrupt file and its working fine, however when I join them toguether and process them it fails… strange! 
Edit: And this is even more strange, I reopened CR, put the 2.2k images again in, aligned and it worked… no unexpected program state, so I guess its not because of image data corruption :?: