JTAG problem with Cyclone IV kit

This error message:

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Error (209031): Device chain in Chain Description File does not match physical device chain -- expected 1 device(s) but found 2 device(s)

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Tells you exactly what is wrong, however, not the solution :)

What you need to do in the programmer gui is to first hit the "Auto Detect" button. This will populate the GUI with the two devices in the JTAG chain. Then double click in the filename area for the Cyclone device, and select the programming file. You can then download to the board.

Cheers,

Dave