Ahhhh, okay -- I understand now; sorry for being dense!
RStudio attempts to compute the screen position of the plot on the screen, and in doing that needs to know the screen's DPI. It seems like we're mis-computing the screen position in your case.
In your multi-monitor setup, what kind of displays are you using? Are they high-DPI displays, or regular DPI?
For what it's worth, I can reproduce this issue when I'm using my laptop's display (high DPI) alongside an external monitor (regular DPI). If my primary monitor is the regular DPI display, but I attempt to save the image while RStudio is on the laptop display, then the wrong portion of the screen is captured (like you describe).