I sent my out of state renewal package in mid-August and already have my new license. They even sent it despite the fact the FBI kicked back my print card as "unreadable". My permit was still good for 30 days and would be suspended if I didn't send in the second card, which I did. Never heard back if it was good or not. Doesn't matter anyway because as long as you pass the background check and submitted two cards, you "did your part". Their words. Besides, if they REALLY need a good set of prints for a shooting in FL or something? They WILL get them then. Besides, it's not like the two "bad" cards are unusable. They can easily tell it's the same person. The prints are probably 90%+ good to go with one or two small things.
Don't know about initial applications. I would imagine they do take longer.