That's probably FT232 going crazy. I have similar issues (but never had to reboot, unplugging-reinserting usb and restarting serial monitor was enough). It seems to be is very sensitive to transients. A bulky 50Hz transformer being unplugged always generates a transient, unless it has a grounded shield inside the coil (quite rarely).
Sometimes, a ferrite bead over the usb cable helps. In my case, when I use a good switching power supply, there are no problems.
I still cant figure out how to protect the FT232 from these transients (I make my own boards).