An Arduino Uno development board is reset when the arduino IDE is first loaded, or the serial monitor is opened, rather that when the IDE is uploading.
I have a solution, which addresses an older problem, as detailed here:
http://playground.arduino.cc/Main/DisablingAutoResetOnSerialConnection
The following two shell commands on FreeBSD will result in the RXTX libraries not driving the RTS/CTS or DTR/DTC handshaking lines on port enumeration (port open, or scanning for available ports on the IDE starting).
Such handshaking results in an attached Arduino reseting when the IDE is opened, rather than a sketch being uploaded. (see url above for full detail).
These commands are persistant between reboots it seems, and cua??.init and tty?? and the same device, just handle Data Carrier Detect differently.
Depending on hardware involved, you make have to open and close the serial port using something like putty for the changes to take effect ("putty -serial /dev/ttyU0").
stty -f /dev/tty??.init -crtscts -hupcl -ixon -ixoff -ixany
stty -f /dev/cua??.init -crtscts -hupcl -ixon -ixoff -ixany
e.g. On my FreeBSD system I use:
stty -f /dev/ttyU0.init -crtscts -hupcl -ixon -ixoff -ixany
stty -f /dev/cuaU0.init -crtscts -hupcl -ixon -ixoff -ixany
Happy to help, just ask!
Kr,
James