I can reproduce the issue consistently. I don't have a small example (yet) however. Are there some Rstudio diagnostics that would be helpful? The lines of code that lead to the call to stopApp are shown below. As you can see from the screenshot, the code to executes cleanly. The required cleanup is done as well when I check the Environment.
message("\nStopped Radiant. State available as r_state and r_data.\n")
stopApp()
OS: macOS Sierra and Windows 10
Rstudio: 1.1.383 and 1.1.412
R: 3.4.2
Interestingly, I cannot reproduce the issue on Linux (CentOS 6.9, R 3.4.3, Rstudio Server Pro 1.1.402)