I recently bought a 2005 LX Civic with a bad head gasket, I changed the head gasket, intake gasket, and timing belt (cars at 86,000). I also reset the valve clearance to manufacturer specifications. After I put everything back together I got more symptoms. The green key light is flashing and the car doesn't want to crank, however, when I plug in my AutoScanner, the immobilzer light doesn't flash and the car cranks up just fine. I'm thinking it could be the relay for the immobilizer or something, but I'm stumped as to why the Scanner overrides the immobilizer. Anyone ever ran into something like this or have any advice? The compression in the cylinders is a perfect 180. Thanks in advance guys, first time a Honda has me stumped like this.

-Yevgeniy

 

Found the problem, it was a corroded ground wire running to the engine block below the thermostat, can't find a way to delete the thread.