Issues after using PCIE USB3.0 hub, long reboot/shutdown

I tried to use PCIE USB3.0 hub with TX2.
After that I removed it.
But PCIE power LED is still on.
After that reboot or shutdown take too much time, compared to before.
Also my startup script in /etc/init.d not working.

The PCIe LED is just a power available indicator…it is “a good thing”.

Not sure what changes you have. Many more details are required to know anything about the script…what is the content of the script (what are its dependencies), where is it located, so on.

To get a log of shutdown you will want to attach a serial console (this is also the best startup log)…this can log all of the shutdown information to your host. See:
http://www.jetsonhacks.com/2017/03/24/serial-console-nvidia-jetson-tx2/