It seems like your config is failing and Auto-restart is configured. From the Cyclone IV Handbook:
"Configuration Error
If an error occurs during configuration, Cyclone IV devices assert the nSTATUS signal low, indicating a data frame error and the CONF_DONE signal stays low. If the Auto-restart configuration after error option (available in the Quartus II software in the General tab of the Device and Pin Options dialog box) is turned on, the Cyclone IV device releases nSTATUS after a reset time-out period (a maximum of 230 s), and retries configuration. If this option is turned off, the system must monitor nSTATUS for errors and then pulse nCONFIG low for at least 500 ns to restart configuration."
John D