Honda Civic - Intermittent startup problems, immobiliser?

Hi, I have a 98 Honda Civic Coupe iLS. When I turn the ignition to position 2 the green key light goes on for about 2/3 seconds then it goes off and starts blinking. When I then turn it to position 3 nothing happens. This only happens intermittently and other times the car starts as normal (@ position 2, green key light goes on for 3 seconds then goes out, position 3 then starts up). I have the original key and a copy that I got cut about 14 months ago. It happens with both keys but more frequently with the original key.

I've read that this may be an immobiliser issue or a problem with the key but why would this happen intermittently and not all the time. Any help/advice would be much appreciated.