JTAG problem with Cyclone IV kit

I am using the Cyclone IV GX Transceiver Starter Board and Quartus 12.1.

The board test system runs correctly.

As I am new to FPGA programming, I followed the Nios II Hardware Development tutorial.

Using the Quartus II programmer, It fails with error as follows:

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

Using the JTAG Chain Debugger, It finds both the FPGA and CLPD.

I also tried loading the demo .sof but have the same problem.

I have followed the tutorial and run on a DE0-Nano with no problem.

The reference manual provides a table indicating S8.3 can be used to remove the CLPD from the chain but I'm not sure that

is the right thing to do since the section on Configuring the FPGA Using the Quartus II Programmer (User Guide) makes no reference to

switch configurations.

Any help appreciated.