Problems after migrating to new server

[windbreaker_familiar]

At any point, even prior to your migration, did you have more content for the affected shows?  More than just season 1 for Seinfeld?  Or have you never had the seasons that are listed in all your shows?  Do you have the missing episode setting enabled?

Nope, only ever had season 1.
I don't think I've ever had the missing episode setting enabled, but trying to double check I can't seem to find it. Is it not under Libraries > Manage Library? 

What happens when you click on "..." for Seinfeld, Refresh Metadata, replace all metadata, replace all images?

So this is interesting. Doing this removes all the extra seasons. I tested some other shows, and I could get the extra seasons to disappear just by doing this on the season itself to avoid messing up my current custom images/metadata. ("Replace all metadata" is unnecessary, "search for missing metadata" without checking replace all images did the trick)
But whenever I run a full library scan, all those seasons just come back.