If the EAP requests don't even come to ISE after the iPhone/iPad wakes up from idle state, then it's probably not an ISE issue. It may be that the AP's are doing some kind of key caching (probably 802.11r or BSS Fast Transition) and that could be broken.
If however you can see the radius request coming into ISE then ISE should be responding to it. ISE will generate the new keying material for the WPA2 encryption.
CCKM is another key caching mechanism but it requires CCXv5 - not sure if that applies to iPhone/iPad (mostly things like Cisco VoIP phones and intel wifi chipsets).
I would open a TAC case quite honestly. They might ask you to disable 802.11r if you have it enabled.