If I were your wife, I'd be pretty frustrated with your pup's behavior, especially since she is the one doing a lot of the daily work/training. And then to have your dog obey you perfectly, LOL, I can see why she's upset! Is there any chance your wife's frustrations are evident to the puppy? That's the only way I can fathom the difference in who she obeys.
Can you implement NILIF and have your wife start treating your dog that way? Also, make the reward for coming (when your wife does it) HUGE!!!
That's all I can think of, I hope others chime in with more help.
Niko: American Showline GSD 5 years old
Rosa: American Muppet Dog (GSD/Border Collie mix) 5 years old