I am not longer on the web team at Stardock. I have moved over to the games team
Sounds like a promotion. Conratulations
Could you please illustrate via a screen capture which logo you are referring to?
It turns out that the problem is that JPG's no longer work but you can still upload a PNG file.
I didn't figure this out until after I went ahead and generated the screenshots so I'll post them anyway. But apparently we lost JPG support and so all the empires that had originally downloaded a JPG are messed up. The empires that downloaded PNG's are OK.
There still are a number of empire's logo's that are affected by this so at the least you should probably remove the text indicating that JPG's are acceptable but I think it would be good if you could get JPG's to work again.
 Actually it appears the problem is deeper than I originally thought. I posted two JPG screen shots as that is the only format supported by the Image hosting site that I use. Actually *all* of the image hosting sites I use only supply JPG format and so I'm unable to post a screenshot because you no longer seem to support JPG's in a post.
The following are the links to the above images.