Could it be a USB cable or a bad PC? Try others for a test.
Some PCs have weak USB power. Some can't produce enough voltage. Does it work better when powered from USB or from flight power though ESC/BEC? Measure the voltage at the FC to make sure it is close to 5V. When flashing, try connecting fligth power to make sure it has enough voltage. Generally, all 4 ESC/BEC should be left unmodified so that they can all power the FC. Don't cut the red servo wire on any of them. Don't disconnect the black servo wire on any of them.
You need v4 bootloader for everything to work in 16.09. After flashing bootloader, you MUST reflash firmware since bootloader updater (bu) overwrites firmware. Flash bootloader v4 then 16.09 firmware. Does that all complete successfully?
Has it been rewired and maybe something is wrong? Have you tried unplugging all accessories like OSD, GPS, aux mag, RC receiver from the FC and see if it runs then?
Are you sure this is a CC3D?
No crash damage? No wrong voltage plugged in at some time?
Have you tried flashing the firmware posted by @f5soh a few posts above this? After flashing, reboot FC it and run it for 30 seconds and then reflash normal firmware.
Was this a ready to fly quad? When it worked, were you running the firmware it came with? Unlikely, but it could be that the mfg made a special version of firmware for it.