I had a similar problem. There was some exchange with the nice guys of Elektron, but we could not identify the root of my “untuned” track 1. I was told that I wasn’t the only one, observing track 1 beeing out of tune, after reloading a project.
In my case it seemed to be a corrupted project and was solved, by creating a new project. I was lucky, because the faulty project was only at its beginning.
I think, it was a bug, which corrupts the project by switching off/on without having saved out everything before … just guessing … because I could remember, I did exactly this … not saving manually.