For the latest UI use
Code:
http://<local ip of computer running content server>:8080/browse
I open the link in Safari, click 'Get' for the book I want transferred, and then specify 'Open in iBooks'.
This works for me running 0.7.46 under OSX.
Make sure that you select the default 'Books' collection in iBooks, that's where all downloads are stored initially.
If what you're saying is that the book is in iBooks, but the cover is not the cover you've added in calibre, that's a different issue. Is that what you're saying?
G