The green light in the dash flashes the whole time.
This is because the immobilizer is disabled in the ECU but the immobilizer unit (around the ignition switch) is still active. Either unplug the immobilizer unit (not recommended) or enable the immobilizer unit in KManager (recommended).
I have purchased a new ECU and need to get it keyed to the vehicle
tech note. Important notes are to 1) enable the immobilizer in KManager once you get to the dealer 2) make sure the immobilizer unit is plugged in 3) make sure you cycle the ignition key after enabling the immobilizer and 4) make sure Honda/Acura uses the 'replace ECM/PCM' function rather than rekeying each key or replacing the immobilizer. If they ask for your spare key you're headed down the wrong path.
I've just got my ECU back and the vehicle won't start
Slow down, don't panic. We haven't swapped your ECU with someone elses. Make sure that all the ECU plugs are in fully (actually unplug and replug them) and that your immobilizer is plugged in correctly. If you don't see the green flashing key when you switch on the ignition then check the immobilizer unit. If you've done any other work on the vehicle to don't blame the complicated box of electronics first - check your work.
I've damaged my immobilizer while trying to remove it
The immobilizer contains a fine wire antenna loop around the ignition barrel. If the wires are broken, then superglue will not fix it. If you think you have damaged the immobilizer while removing it then plug everything back together and verify the engine still starts before sending the ECU to Hondata. (Note only applies to reflashes).
I have a new ECU and my car will not start
Check you have disabled the immobilizer. If you have a JDM ECU then the ECU needs to be modified in order to run the fuel pump.