Yes, there is a known issue when trying to JTAG an EP4SGX290NF45 or an EP4SGX360NF45 device in the Quartus® II software versions 9.1 and later.
When trying to program either of these devices you will get an incorrect JTAG IDCODE error.
To correct this issue you need to update your Quartus II software to at least version 9.1 SP1 and install patch 1.61 or update your Quartus II software to version 9.1 SP2 and install patch 2.15.
- Quartus II software version 9.1 SP1 Linux Patch 1.61
- Quartus II software version 9.1 SP1 Windows Patch 1.61
- Quartus II software version 9.1 SP2 Linux Patch 2.15
- Quartus II software version 9.1 SP2 Windows Patch 2.15
This issue will be fixed in a future version of the Quartus II software.