Strange. It might be that something is missing in the file that the new Reader requires but that is hard to know since the format is secret.
Maybe you should try to add the thumbnail image separately? Or try to use the command line:
Code:
mobi2mobi --addthumbnail image.jpg --outfile res1.mobi in.mobi
mobi2mobi --coverimage image.jpg --outfile res2.mobi res1.mobi