If I remember correctly, and that's a BIG IF, when Computer Magic asked me about fixing the bug, I said "pay me". They wouldn't. Even for the few hours it would take to fix it.
I've thought long and hard about this whole thing, and I can clearly recall FINISHING the 7800 version of the game. Either I was very lucky and none of the puzzle pieces wound up hidden in unsearchable terminals, or ... something happened that I reengineered the code to save RAM and introduced the bug. I need to go back and look at the C64 version and see how it does puzzle pieces.
As for the Blundering Tramiels, well, I don't think it was so much the Tramiels. It was the people who worked at Atari not really giving a crap how they got something finished, just that it was. Which is probably the Tramiels' fault, ultimately, because everyone seemed to be running around like scared rabbits.
It could be that the NTSC 7800's architecture is screwing with how the program code is executed.