JTAG chain not seen unless factory_load switch is set

How to erase it .. I want to restore the braoken card back to how the other cards are ...

The problem is the JTAG chain says it is broken even with inly the FPGA chain enabled. The JATG debug GUI says it

sees nothing if the "factory_load" switch is in the normal position. If I switch to the factory load position, everything work fine.

The JTAG chain is vidible to the GTAG debugger and the Portal Update FPGA code runs as well as the application.

Someone mentioned the FLASH part that configures the System Controller may have been altered or some control bits to that to

put the thing into secure mode and the JTAG chain is disabled.

Via the Portal Update I can commit user configurations to the FLASH but I can't load anything new via JTAG and can't run NIOS load or debug via JATG.

So ... I can try the procedureto restore the facrotey settings

OR

... I can try to dump the entire FLASH and compare the contents with a good reference FLASH dump.

I am pretty sure this was my error but would expect the restore factory settings to fix it.

Thanks, Bob.