Assuming he then tried typing in the seed from the screenshot and didn't just re-enter the newly displayed seed without realising it was different...

Anyway, if he has a screenshot of the seed, then there really isn't a way for him to have created a "different" wallet using the seed from the screenshot... so it would appear that the only logical explanation is that all this time, the user has been using a completely different wallet with a different seed (possibly one that already existed on their computer) without realising it.