Have you set a specific MTU on the APs? They do send jumbo frames I've noticed. If you need the APs or RAPs to send through a topology that doesn't allow giants/jumbos, that's when you set a lower AP/RAP MTU. If on a LAN, leave the MTUs alone I'd suggest. For instance, I set MTU on RAPs so they can get through Cisco ASAs etc.
If you've set an MTU on the AP for a good reason, then what the applications do next matters most.
I wouldn't start playing with client MTUs unless you're trying to resolve a linked issue. You'll make probelms for yourself long term.
If the MTU on the client is the same as the AP, the application (using TCP probably) will try to window up, but SHOULD back off when it hits around 1400-1480 ish. If it doesn't then you have an issue to act as your troubleshooting catalyst.
Cheers.