I'm having the same problem. I haven't figured out how to get this to work even using the latest Rstudio build with pandoc and using .Rmd slides instead of the default Rpres.
I am closer than I was using Rpres, though, because the up and down arrows actually show up when you use the .Rmd slides. Maybe you'll be able to get it to work if you switch?
Edit:
Ok, did a bit more digging. I wish there was a better way, but if you use some non-markdown HTML, you can get down slides (with the pandoc/.Rmd changes as well...)
<section> <h1>Overall Section Title </h1>
# New slide title
# Another slide
---
## Sub-slide
---
## Sub-slide
</section>
All slides within the will be up/down slides.