Did you make certain both the Flats and Lights have CFA checked?
I would configure WBPP in the proper way (based on your thinking) and then generate ALL of the WBPP screenshots using the diagnostics button. Your manual screenshots are not enough (and the window isn't stretched in length enough). The auto generated ones will not have this issue.
I went in and manually checked CFA for the Flats and that didn't work so I tried again and in addition to checking CFA on the flats I also changed the Mosaic Pattern from Auto to RGGB on the calibration tab and then it worked fine. The images were from my ZWO ASI294mm Pro OSC camera.
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