Thank you so much for your reply and the explanation! It's really great getting help from you.

(And Calibre is awesome, thank you for it)
What you said make sense, but I wish there was some way to find out which book is the problem...:\ Is it safe to assume the problematic book is one of those who keep re-transferring, though? (pleasepleaseplease) Or could it be any of the books whatsoever?
Also, do you think Amazon might be able to get diagnostics from the indexer? Or shouldn't I even try ask them..?