Cyclone III Initialization issue

[Altera_Forum]

Hi, 

 I am using Cyclone III [EP3C16] on my custom built board. I programmed the device with a simple .sof file using Quartus II 9.0sp2 Web Edition via USB Blaster. I see the CONF_DONE pin high after configuring and the Quartus say success. But the FPGA didn't work:( The INIT_DONE pin is also not returning to High [have made software configuration for using the INIT_DONE pin].   I have made sure the following 1) Proper power supply 2) Proper External Clock to the FPGA 3) Have made the JTAG connections [support for both JTAG and Active serial] as per the Altera's suggestions 4) I was not sure whether JTAG module needs to be supplied with 3.3V or 2.5V. I tried both, but still the same issue. 5) nStatus and nConfig pins High   When I use SignalTap, it is able to download the .sof, CONF_DONE goes High. But when I try to Analyse [RunAnalyse/AutoAnalyse], SignalTap says "JTAG Communication Error" and also says "instance not found".   I understand that the FPGA is getting configured but not initialized.   What am I missing here? What should I do to make the FPGA work?   I request you people to help me getting out of this issue.   Please let me know if you need any further details to find out this issue.   Regards, Jaga

[Altera_Forum]

Sounds like the FPGA looses it's configuration. One possible reason is either in NCONFIG driven low or a conflicting action of the on-chip configuration controller. The latter can happen, if e.g. an unconfigured AS device is connected to the FPGA. There's a Quartus programmer option to halt the on-chip configuration controller. Another possible reason is momentary drop of a power supply below the POR threshold.