mnr posted this (rpresentation vs mathjax & preview pane) in early June with no replies. I never had any issues until I upgraded both R (from v3 to v4) and R Studio, and now I have the exact same problem as mnr.
I feel the live MathJax engine isn't properly linked to the Presentation pane, because if I use a browser to open the HTML version of the presentation, the math looks perfect.