You may have run into the same problem I asked about last night (and to which I have not yet received any reply).
I'm assuming the images captured by the ZWO were in a format other than .xisf, and were converted to .xisf as part of the batchpreprocessing script. My current hypothesis is that batch script does NOT embed image properties (including the CFA pattern) when it saves to .xisf.
If so, it seems to me the solution is to get the batch script to embed the properties while saving to .xisf. However, I'm just not smart enough, or have the skills, to solve that problem (assuming that is the issue.)