UPDATE 20AUG13: This was submitted to QT Support. Here is the reply:
“ Unfortunately this is working as designed. R&D changed how the passwords are hashed for Custom users between version 10 and 11. In version 11 they switched to a much more complicated and secure hash, and since hashing is a one-way operation, QlikView cannot convert the passwords.
The only option here is to manually enter every user's password.”