I've opened an issue regarding that in the GitHub repository. I'm not sure why the wpseo option contains the wrong options in your case, but this may well be something that has happened to more people somewhere along the upgrade-route.
I'm proposing a one-time option clean-up in the next upgrade, but want to discuss this with Yoast first.
In the mean time, there should only be a few options saved to the wpseo option, mainly the things which you can set on the SEO->Dashboard page and some of the ignores for the tour and such.
You could probably just empty that specific option (not delete, just empty) in the database and all should be well again. You will need to set your preferences on the dashboard again of course and you will see the tour pop up again, but that's nothing major, or is it ?
Hope this helps!
Smile,
Juliette
P.S.: could you mark this topic as resolved ?