Cory,
I've not experienced this and I've got several WS-C3560-48PS-E deployed providing power to access points. These are at remote clinics which lose power frequently due to the midwest (US) thunderstorms.
I've never had to activate the PoE section of the switch, I'm not even sure what that is. When the power is returned, the APs boot up.
If you have access to the switch, verify the model number (show version) and verify the PoE settings (show power inline). It should return something like the following:
Interface Admin Oper Power Device Class Max
Fa0/46 auto off 0.0 n/a n/a 15.4
Fa0/47 auto on 4.4 AIR-AP1230B-A-K9 n/a 15.4
HTH
Steve