Hi kdemoree,
there are differences how the attributes are mapped in SHP and GPML files. Depending on how you have captured the gpml:AverageAge in the shapefile attributes, you might have to use a different attribute name. GPlates in general encapsulates the shapefile attributes as gpml:shapefileAttributes:YourAttributeName. So even if your shapefile has an attribute called FromAge and GPlates has mapped it directly to the ValidTime from values you can query in the main window, you will still have to point the ColorByAttributes part to the gpml:shapefileAttributes:FromAge (This is a bad example as it might be different in the age/plateID assignment cases, but I am fairly certain that this is true for most of the other attributes - @john.cannon pls correct me if this is wrong).
So this means that for the GPML files you should be able to directly access an attribute such as your gpml:averageAge by using that attribute name in the ColorByProperty script with your CPT, whereas in the shapefile case you might have to use gpml:shapefileAttributes:averageAge (or whatever your gpml:averageAge attribute is called in your shapefile).
Hope this helps,
Christian