Programming JIC files using qaurtus_pgm

It seems to be working for me. I've shown the text from the console below:

As a side note, You may want to consider using a NIOS processor and the nios2-flash-programmer.exe utility instead. It's much much much faster than using the JIC method. We use that method for programming our boards in manufacturing.

C:\Projects\trio\fpga\trio_top\altera>quartus_pgm trio_top_jic.cdf
Info: *******************************************************************
Info: Running Quartus II Programmer
    Info: Version 8.0 Build 215 05/29/2008 SJ Full Version
    Info: Copyright (C) 1991-2008 Altera Corporation. All rights reserved.
    Info: Your use of Altera Corporation's design tools, logic functions
    Info: and other software and tools, and its AMPP partner logic
    Info: functions, and any output files from any of the foregoing
    Info: (including device programming or simulation files), and any
    Info: associated documentation or information are expressly subject
    Info: to the terms and conditions of the Altera Program License
    Info: Subscription Agreement, Altera MegaCore Function License
    Info: Agreement, or other applicable license agreement, including,
    Info: without limitation, that your use is for the sole purpose of
    Info: programming logic devices manufactured by Altera and sold by
    Info: Altera or its authorized distributors.  Please refer to the
    Info: applicable agreement for further details.
    Info: Processing started: Tue Jun 17 14:36:04 2008
Info: Command: quartus_pgm trio_top_jic.cdf
Info: Using programming cable "USB-Blaster "
Info: Started Programmer operation at Tue Jun 17 14:36:09 2008
Info: Configuring device index 1
Info: Device 1 contains JTAG ID code 0x020E40DD
Info: Configuration succeeded -- 1 device(s) configured
Info: Device 1 silicon ID is 0x16
Info: Erasing ASP configuration device(s)
Info: Programming device(s)
Info: Successfully performed operation(s)
Info: Ended Programmer operation at Tue Jun 17 14:40:34 2008
Info: Quartus II Programmer was successful. 0 errors, 0 warnings
    Info: Peak virtual memory: 321 megabytes
    Info: Processing ended: Tue Jun 17 14:40:34 2008
    Info: Elapsed time: 00:04:30
    Info: Total CPU time (on all processors): 00:00:14