Altera® specifies each individual power supply on Cyclone® III devices should reach the recommended operating range within 50 ms as described in note (4) of table 1-3 of the Cyclone III Datasheet (PDF).
As the Power-On Reset (POR) time for Standard POR ranges between 50–200 ms, you need to ensure that the power supplies have ramped up prior to POR. If you cannot meet the maximum VCC ramp time requirement of 50ms, you must use an external component to hold nCONFIG low until the power supplies have reached their minimum recommended operating levels. Otherwise, the device may not configure and enter user mode.