Quartus II 11.1sp2 programmer does not recognize EPC2LC20

Thanks for clearing up the problem.

What the failing jtagconfig --debug report shows is what jtagserver read from the chain when it tried to auto-detect it. jtagserver does the following operations:

1. Go to TEST-LOGIC-RESET state (this selects the deviceid register on devices which have it or the bypass register on devices which don't)

2. Do a DR scan to read the value scanned out of this register - try and identify the ID codes

3. Do an IR scan to check the length of the combined register. Load all ones into the IR to select the bypass registers on everything

4. Do a DR scan to check that all bypass registers behave properly and to confirm the value read back in step 2

The values read out suggest that there are two devices on the chain (bypass register length 2 - deviceID lengths 1+32, IR length 1+10), one of which is behaving very strangely. If these values don't match the actual chain on the board then some sort of signal integrity issue is likely (as you have found)