jim,
When you load an image into PI it will look like that initially, what your seeing is the bayer matrix. The colour information is stored within the file but you will have to use the process called 'Debayer' to apply it. You will have to select the correct 'bayer/mosaic pattern' for your camera to have the colour displayed.
For a Canon 6D it should be: RGGB
(You'll always know if you choose the wrong pattern as the colours will be all wrong and you'll still see a bit of that checkerboard pattern in the image)
Your Canon software is automatically debayering your image when you open it up as this is generally what you will want from standard daylight images.
The difference here with PI is that most of your preprocessing of Lights, Darks, Bias and Flats will be performed in their non-Debayered state (as your seeing your image now), you will only debayer your Lights and that will be only just before you perform Star alignment ready for the final integration.
Hope that helps
Paul
