I was worried, too. Then I got a packet from case showing they had everything except my LORs. They still haven't cashed my check, though (nor has any other school). My guess is certain schools won't cash it until your app is complete...
I take that back...my check went through today! The time between getting that packet and my check going through is pretty much on-par with what AADSAS told me the turn-around would be for schools to get my LORs...So I'm guessing, at least in Case's case (haha, sorry for that), they wait until they have your complete app before processing the fee.
I'll probably get a rejection letter tomorrow, haha...