I've identified what seems to be a bug with the Visual Editor mode.
I am working on an RMarkdown filein Visual Editor mode and also have another source pane with some code open.
When place my cursor onto a line of code in the RMarkdown fileand try to run it by hitting Ctrl+Enter, it instead tries to run the code in the other source pane, even though my cursor is in the RMarkdown document.
Switching the RMarkdown file from Visual Editor back to Source Editor solves the problem, which makes me think it might be an issue with the Visual Editor mode.
Another (possibly related) issue I've found is that when in Visual Editor mode, using the History > To Source button does not work for transferring code from History to RMarkdown. Again, this is fixed by switching RMarkdown back to Source Editor mode.