This is actually quite pervasive and difficult to get rid of. You can regenerate the Thumbnail all you want, save, resave, rename, push in new projects, change and create new Family Types, purge ... it's still there. The family remembers that initial image somehow. Really, really strange.
Here is a bit of information that mentions the discrepancy between file thumbnail preview and Type selector preview:
https://graitec.co.uk/blog/entry/revit-thumbnail-orientation
It seems it's the View Cube that dictates the Properties Box View orientation but that's about it. The Type selector will always show an Isometric, Shaded view of your Family Type as set in the Family (instance parameters are taken into account). That's my understanding for the time being.