Going back a bit here mate.. but isnt there a 7407 or similar that acts as a buffer chip to PIA? Is a straight gate.. signal comes in as "high" and exits as "low" ( or vice versa). Id be looking here
Im pretty sure that in test mode Williams games do not recreate what would happen in a real life scenario there are some oddities thrown in.
Also check that if a STRAIGHT 7XXX chip is listed you havent put in a 7LSXXX... the fan out is not enough.. you do require an actual straight 7XXX if listed... been there myself!