In my case it is almost 100% reproducible by doing the following step of actions:
1. Start Rgui.exe
2. Update some packages by update.packages(ask=F, checkBuilt=T)
3. Minimize the R gui during downloading of package files or move to another virtual screen (I'm using VirtuaWin)
4. Exit R by either typing quit() in the console or by presing the X button on the main window
When step 4 is finished, the Rgui.exe process will continue to use 100% of one CPU core until terminated from task monitor.
I'm not sure if step 3. above is relevant or not, but that is my typical use case.
I've found an ancient record that describes the same behavior: http://grokbase.com/t/r/r-help/0353emb90w/r-memory-leakage
Still happening on R 3.2.2.
One additional observation. If I wait 10 seconds or more before closing Rgui.exe after upgrading of packages the process exits as expected. No aberrant continual CPU usage happens.