Is there a known issue with Cyclone III or Cyclone IV devices if a user reset is deasserted before the device has entered user mode?

Due to a known issue with Cyclone® III and Cyclone IV devices, unexpected register output behaviour may be caused when a user reset is deassserted before the device has entered user mode.

To avoid this issue, Altera® recommends you deassert user logic reset after the device has entered user mode, or enable the clock source to your registered logic after the device has entered user mode.

The INIT_DONE signal can be used to indicate that the device has entered user mode. If the INIT_DONE signal is not enabled, refer to the tCD2UM (CONF_DONE high to user mode) parameter in the device handbook.