When you tell the XBEE to go to sleep (via changing the sleep pin when SM=1 or 2) I believe it performs any waiting samples and uart/RF data, then moves a pin to indicate it has gone to sleep.
Then when you change the wakeup pin to wake the xbee up, you have to wait for the xbee to move a pin declaring it is awake and functioning, and then you are supposed to wait X amount of time.
It moves the CTS pin to indicate sleeping/wakening
Going to sleep:
When Sleep_RQ (pin 9) is asserted, the module will finish any transmit, receive or association activities, enter Idle Mode, and then enter a state of sleep. The module will not respond to either serial or RF activity while in pin sleep.
The module will wake when Sleep_RQ is de-asserted and is ready to transmit or receive when the CTS line is low. When waking the module, the pin must be de-asserted at least two 'byte times' after CTS goes low.
Those are from the manual for the 802.15.4 modules, so they might not be valid.