It isn't exactly a user-friendly feature. No one is expecting to have their temporary directory explode. I didn't think there would be any harm in reporting this behavior.
You are right.
Lets try to investigate this a little.
1) Which version of the Arduino IDE are you running.
2) Which version of the operating system are you running
3) 32bit or 64bit
4) When you start up the IDE from the commandline it prints the version information for the RXTX library. What version is installed?
5) How did that happen ?
I left the Arduino IDE open overnight with the serial monitor window open (And no Arduino connected)
You had the serial monitor connected to the board and then you simply unplugged it ?
6) Can you replicate this error?