If the System-app version changed then such restore can lead to troubles.
Only safe bet is to restore the XML-Data (yellow with XML symbol).
That is why I always set the accounts manually, wifi call logs and sms I always export as XML. For additional things (like calendar and bookmarks) I use a mix of Titanium Backup and Super Backup.
So to make it short - nope, you didn't miss anything in the procedure :-)
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