The Protein Quality report is dependent upon the amino acid data available. Amino acids are reported for USDA foods much more so than brand-name foods. Manufacturers don't widely report amino acids because it is not required to do so for Nutrition Facts labeling. If amino acid data is missing for the foods you have chosen, the Protein Quality report will not represent the foods properly.
MyPlate values are available for most foods in the ESHA database. Exceptions include Canadian Nutrient File and UK database foods. Also, if you have added new ingredients to your software, you would need to populate the MyPlate fields for values to be included.