Why would original NES-039 controllers work but NES-039 not?

Greetings:

My original NES still works, and I am convinced it's because I sent it to Nintendo 15-20 ago when they offered their refurbishment program. When they sent the console back they included two new NES-039 controllers.

I don't specifically remember if I tested the NES-004 controllers I already had when I received the refurbished unit or since. However, I recently tried to play FF1 with the NES-004 and could not move past the title screen. I tried the NES-039 controllers and they worked fine. I should add that I purchased some used and working NES-004 controllers from a reputable reseller and they didn't work either.

Any ideas why the NES-004 would not work but the NES-039 would?