Quick update. Finally managed to get Super Mario Brothers to start on the NES emulator without having cheat in the debugger. Turns out that I had misread some documentation and so I was sending hex 0x42 to represented the unconnected controller #2. After running through the debugger over and over I’m pretty sure it was getting interpreted as every key being pressed on that second controller. In any case, it was definitely interfering with the START key detection (since the actual game played fine once started).
Moral of the story is the 42 is not always the answer especially if, as a co-worker said today, you’re not asking the right question.