Issue with unreliable controller input

Well, I can't really answer the controller question, but you can just make the dialogue box advance automatically without input. That's command $48 instead of $4B; it's the same one that gets used in the intro.

For example:

Code:

CC98FA: {48-09-40}            Display dialogue message $0009, continue executing commands (Show text only) (At top of screen) "Can it be that those   in powe..."
CC98FD: {95}                  Pause for 120 units