I just updated to the latest release of PI.
I ran a new set of images (lights, darks, flats, bias) and discovered that the something in the BPP process is inverting the light image. As a result, instead of the flat removing the anomalies, they are added to the light.
What???
The attached image shows the flat master, one light frame, and the output of BPP.
I know, I have to retake my flats - I did a very poor job of setting my light panel at the right distance and didn't bother to check before continuing. Live and learn. But it still shows the horrible condition of the camera - which I'm sure I can rectify as well. I'm not as concerned about that as I am about why the light image is being inverted in the BPP process.