If I can assume that you have a Access Point not a combo AP/Router I have had a similar issue.
I cannot understand, though, how the access point can utilise an IP helper command anyway. Forgive me if I am wrong, but the AP is a Layer 2 device (bridge) and therefore I can't see any way that it can get involved in DHCP (A layer 3 protocol). I notice that it is spoken about in the IOS notes, but I still don't understand how it works.
You are best making sure that you either have a DHCP server on each VLAN or configuring the IP Helper command on the VLAN interface of the router.