Hi Daisuke,
The PCIE interface for the C6657 is not designed for hot-swap operation where the signal is driven from one side before the power is present to the SOC. We have seen boards designed for the lab environment that are connected with SMAs where one side is powered while the other is not but this is not recommended for production systems. You should design your power supply to begin sequencing once the PC power supply is present or you should add a component which will prevent the PCIE from driving the receiver before the C6657 power is present.
Regards, Bill