Sounds weird. If the elements appear in the tree in the Structure View, they should also show up in the canvas, of course...
Would it be possible for you to upload your GraphML file here? (See How to upload files to yEd Q&A? for related documentation.)
You can also inspect the elements yourself, of course:
When you double-click an element in the structure tree, that element will be centered in the canvas and also be selected. Now you can inspect the properties of the selected element in the Properties View (coordinates, width, height, color, etc.) to see what is maybe wrong with it.
You can also do a 'select-all' (Ctrl-A) and change all elements to have, for example, a uniform size of 30px width and height, or black color, etc.