Wel when I first went to your site before I could see the image in the bottom right and it seemed normal. But now I don’t see anything so maybe you have removed the ads.
If you mean that it’s cutting them off, it displays the grid in an iframe so if you are sizing it too small then it could be cutting them off. If they are actually showing as transparent then maybe its something to do with the GD setup on there. Are you able to attach one of the original images you are uploading which causes this to happen so I can test it on another install?