Quartus II 11.1sp2 programmer does not recognize EPC2LC20

... while I would still appreciate any feedback on the jtagconfig --debug responses above, I did want to close the loop on the thread regarding what was found to be the issue ...

I took the boards to the customer's site and found that even with their USB Blaster the JTAG interface was not functional. The customer had a "Byte Blaster" setup, and with that we were able to access the EPC2 devices.

What was found to be the root cause was 5V clamping diodes that were installed on TCK, TDI, TDO and TMS. It is not clear what problem 5V clamping diodes would cause, most likely an excessive capacitave load of some sort. With the diodes removed the USB Blaster reads the correct ID code and can read and program the EPC2 device.

Thanks again for the earlier support!