Jean Guy, since you are running the Batch Preprocessing script, have you tried to run the Diagnostics button, rather than the Run one? So far I am not finding any problems with the FITS. I have looked at the headers and I parsed through them with 'od' and they are just fine and legitimate.
I am going on the idea, right now, that it is the script that is barfing for some reason... and I am hoping that the Diagnostics will give a better listing of what the script is doing when reading the files.