If that's what happened then when he re-enters the seed to verify it Electrum would reject that.
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.
Pretty sure this is correct. Makes sense now. Going to try to brute force the PW and hope I remember enough of it to be able to brute force it.