@adrienneltravis,
This is an interesting question.
CropRefine works simply by reading the contents of your uploads directory and organizing crops/resizes of images in a pile under the original. If you register a new image size for WordPress to observe, but have uploaded images beforehand, the instruction for WordPress to create that image size was not yet present, and CropRefine wouldn’t find that not-yet-existent image.
It’s possible that future releases of this plugin could also interpret registered image sizes/crops, and inform WP admins that one doesn’t yet exist and should be created (or further yet, automatically create a new image size based on these new instructions), but at this time, that’s not a feature. The plugin only gives admins the power to refine existing crops.
Until this time, we recommend using the Regenerate Thumbnails plugin (to iteratively create the new image sizes en masse), and Crop/Refine if you need to adjust them individually.
ERA404