I made this picture of isometric sand castle that uses gradient and when I save this image, the saved image, irrespective of the format, is transparent in some areas. There is a hue of some sort. The entire image is not this way only parts of it. The image is opaque and not intended to be transparent at all, I have used transparency on the gradients, if that means anything. There is no significant difference I can find on objects that appear as they should and objects that have become transparent. Oh and the objects all have their outlines, there is just no fill appearing.
Add an extra layer under all your artwork layers which is completely opaque and visible. Alternatively you can store your image in a jpeg format. Jpeg images don’t have any transparency.