iPhone 6 restored from encrypted iPhone 5S backup doesn't retain passwords
I just have had the same issue when I try to restore 5S backup into 6. After a few attempts, it eventually worked fine. Here's what I did for the successful try:


Take old iPhone backup with encryption on
Reset all content / all settings on new iPhone without connection to PC / Mac
Go through startup config on new iPhone until you see "Set Up iPhone" screen, which let you select the options to restore from iCloud / iTunes backup
Select "Restore from iTunes backup"
Connect to PC/Mac and select backup you want to restore
Done!


It wasn't successful when I tried to restore without reset, or without going through startup config. Hope this helps