Arduino Mega not flashable with XBee PRO S2B
I don't have a PRO to play with, but I just looked at the datasheet and it appears that it SHOULD timeout after 60 seconds 


  If no serial transaction is initiated within a 60 second timeout period, the bootloader times out and returns to 
  the menu. If the upload is interrupted with a power cycle or reset event, the EM250 will detect an invalid 
  application image and enter bootloader mode.  (page 139)


Also, it seems that it takes a particular set of conditions to get to the bootloader, obviously these conditions are being met:


  XBee modules use a modified version of Ember’s bootloader. This bootloader version supports a custom entry 
  mechanism that uses module pins DIN (pin 3), DTR / SLEEP_RQ (pin 9), and RTS (pin 16). To invoke the bootloader, 
  do the following:
  
  
  Set DTR / SLEEP_RQ low (TTL 0V) and RTS high.
  Send a serial break to the DIN pin and power cycle or reset the module.
  When the module powers up, DTR / SLEEP_RQ and DIN should be low (TTL 0V) and RTS should be high.
  Terminate the serial break and send a carriage return at 115200bps to the module.
  If successful, the module will send the Ember bootloader menu out the DOUT pin at 115200bps.
  Commands can be sent to the bootloader at 115200bps.
  
  
  Note: Hardware flow control should be disabled when entering and communicating with the EM250 bootloader.


Perhaps check pins 3, 9 and 16 on boot and see if you can modify their behaviour.