Hi there,
So I've got what seems like a bug with the Mac IDE (using v15): If the IDE is running and you tell the computer to restart, the Arduino IDE will quit, but the OS will put up a dialog say "The application Arduino has canceled the restart.". This is with Mac OS X 10.5.6.
Seems like it's handling the "request restart" message, but is replying "no, stop!" when it should be replying "yes, proceed!".
-Paul
It's not just 15 that does this, I find it happens on 11 as well so it looks like it has been in a long time.
Check the OS X system log to see if anything is being reported there. It appears that the running JVM is not accepting the (equivalent of) HUP or INT being sent to it. Since it cannot shut down cleanly of its own accord, the OS rightly abandons the shutdown.
Depending on how the VM is launched by the system UI server, it may be that the Arduino JVM process proper has been disconnected from the parent somehow.
BTW, even Safari failing to shutdown cleanly will cause OS X to abandon a restart or shutdown. I bet the arduino is throwing up a modal dialog (or the whole IDE is behaving like one.)