Thanks for taking the time to generate a trace -- unfortunately, it looks like the R session wasn't doing much of anything during this time. (It's possible that RStudio was running code separately from the R session that's responsible for this slowness, though.)
There's one other thing I could suggest, although it would be a bit time consuming. We publish daily builds of RStudio here (these are installer-less versions; you can just unzip them on your desktop and then run the file at bin/rstudio.exe within).
For example, you can download RStudio v1.1.340 using this link:
https://s3.amazonaws.com/rstudio-ide-build/desktop/windows/RStudio-1.1.340.zip
and can download other builds by replacing the build number in that link. If you have time, would you be able to test a range of RStudio releases, to see which particular build seems to have introduced the slowness you're observing? (You could imagine this as a bisect -- start at version 170; if the issue reproduces, try version 85; if not, try 255; and repeat the process until the bad build is found.
If you're able to discover the build in which the slowness was introduced (or even narrow it down to a range), that could be very helpful.