ADE uses 90wx130h pixel thumbnails, if your cover image doesn't fit well within that aspect ratio, ADE will usually add a white border instead of crop, so I'm not sure what's going on there.
For your personal use you can change the thumbnail for any book within ADE by replacing the appropriate .png file in the Thumbnails folder inside of your Digital Editions folder.
It seems if I upload a 130 pixel thumbnail initially, DE "remembers" the small size
and displays the thumbnail properly. However, if I upload the standard size
cover image (600 x 900) DE will crop the thumbnail.
Thumbnails display O.K. in all other ePub formats.