Thanks for the report. I don’t think we have anything quite precisely like this documented. The closest I can think of is this one, which describes a scroll offset problem when using navigation tools to jump between sections in the an existing scrivenings session. We do have a reproduction for that one, at this point. The symptoms you are describing certainly do fit that profile, but not the trigger.
This ‘unaligned editor’ thing is a new issue, though, because the last time I viewed it in Scrivenings, it worked fine.
So the question then is, when was the last time? Was it over a year ago, when you were using a version prior to 3.1.6, or more recently? If the latter, then something about the content or the settings applied to how you view Scrivenings mode, would be the first suspect. Anything you can think of along those lines would be helpful. Speaking on the one I linked you to, we found a binary correlation between the use of View ▸ Text Editing ▸ Show Titles in Scrivenings menu toggle, and whether the bug can be triggered. Other things might make it worse, or even be necessary, but that one seems to be the strongest trigger.