I think we might need a bit more information here. Are you saying that it does not copy ALL the albums when you do the backup? And every time you do it, it starts over with the same albums but does not finish?
One thing worth pointing out again, although probably not related to your problem:
The Backup command (with a capital B) is reserved for those who need backward compatibility with an old JB7 unit. Otherwise the backup command to use is Export. Often times, we use the word backup (lowercase b) generically, which can be misleading. Normally, use the Export command (with companion command Import).
Back to your problem... What version of software are you on? Not too long ago, problems with the Export command were discovered and fixed in a recent version of software. If you're not up to date, please do a Web Upgrade and then try the backup again.