I have noticed, in the last few months, that some Theme's reset their settings during a website migration.
I've been working in WordPress for like 8 years so this is definitely new, and it's happening with sites that I've never managed before the migration so there's no clear pattern I can identify.
It's insanely frustrating because I'm just cloning the files from one server to another and exporting/importing the MySQL database respectively. No files are being left behind that I'm aware of, no changes to the database file beside updating the URL.
Here's an example:
Broken: http://makecontest.theportlandcompany.com/
Working: http://www.makecontest.com/