Quartus II Programmer fails with message: CONF_DONE pin failed to go high in device 1

[Altera_Forum]

I am trying to uploa .sof file (of DE2 control panel) to DE2 board (that uses Cyclone II family EP3C16F484) 

 I am using Quartus II 13.0sp1 in an Asus S46C Ultrabook with Windows 8 64 bit.   I use Quartus II (64 bit) Tools/Programmer and standalone Altera Programmer (32 bit) with same results, with the messages:  Error (209014): CONF_DONE pin failed to go high in device 1 Error (209012): Operation failed   I tried other .sof files from examples without success.  I tried in a Windows 7 machine with Quartus II 10.0 with the same results.  --  Airton da Fonseca Granero

[Altera_Forum]

Ok I screw up: the manual says: Set the RUN/PROG switch to the RUN position. 

I thought it must be in PROG position, but it seems if you use JTAG this is not the correct setting.  Sorry.

[Altera_Forum]

Hi,  

I have the same problem with a Terais DE3 board, using Stratix III. However, the FPGA seems to be programmed correctly, because the CONF_DONE Led on the board goes on. After pressing "Auto-detect" in the Quartus programmer GUI the verilog program is executed on the board, i.e. Leds are blinking correctly and whatever should happen happens! So the error seems not to be the programming itself but only the programmer receiving the CONF_DONE signal. The board worked fine for long but someday this error popped up. I tried different DE3 boards with the same PC+software and this error appears only with one specific board, so it is obviously a hardware error.  Are there devices on the DE3 board sensitive to ESD or mechanical stress which, when defect, could cause such an error? Is it possible that something in the ROM (?) of the FPGA, gets corrupted due to an unsuccesfull programming attempt (power loss or whatever) that could cause this error? Any idea?  Thank you!