I've got a CM3 module which is working perfectly, and I received my second CM3 last week and I've been trying to clone the first to the second with no luck.
I start with the first CM3 and ran:
sudo apt-get update sudo apt-get upgrade sudo apt-get dist-upgrade sudo apt-get install rpi-update sudo rpi-update
sudo apt-get update sudo apt-get upgrade
after reboot. And the first one still works. Then I put the first one into my CMIO3 and make an image using
sudo ./rpiboot sudo dd bs=4M if=/dev/sdb of=cm3.img
Wait a couple of minutes until the image creation finishes and switch the modules off, disconnect and connect the second CM3 module. Write the img to the second module
sudo ./rpiboot sudo dd bs=4M if=cm3.img of=/dev/sdb
After dd finishes I disconnect the USB slave cable, disconnect and reconnect power cable and both POWER and ACTION LEDs stay solid red and green respectively.
Using Raspbian Jessie. Kernel 4.9.33-v7+