Peter,
With Astro Pixel Processor (if that is what you mean by "Astro Pixel Pro"), before you begin processing FITS files from a color camera (I usually do that even before I load the image files in step 1), select the step 0 tab that is titled "0) RAW/FITS" on the left panel, and enable the "force Bayer/X-Trans CFA" checkbox.
With ZWO's camera, if the colors don't look right, choose RGGB in the "pattern" menu above the "force Bayer" checkbox. Otherwise, you can usually just leave the "pattern" menu at "supported."
Chen