Cyclon III starter Kit, flash device

The can't recognize silicon id for device i isn't related to JTAG but to the flash loader IP. It's also using JTAG, but if the FPGA is recognized at the JTAG chain, it's probably not a JTAG problem. A possible reason is, that the present FPGA configuration doesn't contain the PFL IP or is conflicting with flash programmer operation somehow. In this case, the factory default parallel flash loader should be loaded instead. It can be found in the \quartus\common\devinfo\programmer directory.