Java + JSSC + Arduino + Windows
I had this problem with communication with Arduino Uno (I think that the Arduino Uno, and other boards, with this type of scheme, suffer this problem). 

The DTR line on Arduino Uno is connected with RESET, including when you use the Arduino IDE Serial Monitor port, such that the parameter of DTR is false. Yeah, you can fix this with capacitor or catch place RESET EN on board. But when you set setting you can just write: 

comport3.setParams(9600, 8, 1, SerialPort.PARITY_NONE, false, false); 


The last parameter is DTR and its default is true, the second to last parameter is RTS (it defaults to true too). I set both of these parameters to false and my board reads commands from the computer without resetting.

I write this for other people who had this problem.