Did you maybe bump the Light Green/Red wire there also? Thats the neutral switch wire. Unplugging the Black/Red wire for the ignition wouldn't affect the neutral light at all, at least it shouldn't. The neutral light is powered by the battery and the ground to the bulb is switched by the neutral switch. My guess is there is a bad connection there causing problems.
---------------------------------------------------------
1984 Honda ATC200ES "Big Red"
1982 ATC200E "Hondie"
1988 TRX300FW "Project Quad" Still in progress....