As Image Magick develops, things change and we can not do things the same way we did before. This is an update to paint on tranparency.
To paint on transparency it must be changed to opaque transparency. Set the method to Floodfill.... The paint type to Matte and the color to white. Click on the transparent part you want to paint. It will change to opaque white.
Now set Method to Floodfill, the type to Color, and the color to whatever you want. Now click on the same part as before. It should color.
In some rare instances it may not turn opaque white but black. If it does just continue on with Floodfill color and your desired color. It should change to your color.