Issue on Serial Port Communication (in JAVA)
The serial flow control signals (DTR and/or RTS) must be set accordingly to the Arduino specification and to the specification of USB-SERIAL adapter you're using.

Looking briefly at the schematic of your board, I can see that the RTS signal is disconnected, but DTR signal from FTDI chip is coupled with the ATMEGA's RESET pin (I imagine that this is done to allow Arduino uploader to reset the micro and upload new firmware to it).  

This means that you have to set DTR signal (in your Java code) to avoid unwanted resets.