You may get this Critical Warning message, when targetting a Stratix® V, Arria® V or Cyclone® V device and you have not enabled the optional INIT_DONE function in your Quartus® II project.
In Active Serial (AS) multi-device configuration mode, Altera recommends that the INIT_DONE output pin option is enabled in the Quartus II software for devices in the configuration chain. Do not tie INIT_DONE pins together between master and slave devices. Monitor the INIT_DONE status for each device to ensure successful transition into user-mode.