I have one specific logo that is semi-transparent at the top and bottom - the server is being far to aggressive when it trims away the transparent edges and some of the image is disappearing as well.
This is the logo:
Sourced from fanart tv - here.
And here's what it looks like in ET (same issue in the WebUI):
I've tried replacing it a couple of times, and the top and bottom disappear just after I add the image.
Here's what it should look like (on a black background):