When in settings, the bar that resizes the file tree, and the editor, is shown above the modal. Seen here:

The modal had a z-index of 20. Bumping it up to 30 fixed it, as seen here:

I can put in a pull request on this tonight, let me know what you think!
This is great! I always thought my screen was broken when I saw this line, good that we can finally fix this issue.
I always thought my screen was broken ...
馃槅
@CompuIves Seems like this issue can be closed
This issue still exists:

I'll submit a PR now.