Check above the pedal area on the brake. There is usually a depressor switch there that reports to the locking mechanism. Check to make sure the pedal depresses the depressor switch. I don't know if this switch is on Honda automatics, but it's on almost every other car I've seen.

Just north of where you put your foot on the brake. Look up there for a switch of some sort and if there is one, be sure it is aligned with the brake pedal shaft.