Hello jmgc,
CR2 is a proprietary format and may have certain variations depending on the camera used. If you are observing the problems with the visual representation when the images are opened in Metashape, please send the examples from the corresponding cameras to support@agisoft.com, so that we could study them and adjust, if possible, the RAW data import.
In general case, however, it is recommended to process RAW images to TIFF, for example.