I posted some fixes on ladyada.net at the end of last year for fixing the handling of the RTS serial line in the Linux Arduino software when using a Boarduino board with the FTDI serial adapter. Details are here: http://www.ladyada.net/forums/viewtopic.php?t=4703 I've been asked to post the fix here as well.
In src/SerialImp.c in the RXTXComm package, I changed the line
ttyset.c_cflag = CREAD | CS8 | CLOCAL;
ttyset.c_cflag = CREAD | CS8 | CLOCAL | HUPCL;
That's line 303.
And in ser_posix.c in the Avrdude source, I changed
termios.c_cflag = (CS8 | CREAD | CLOCAL );
termios.c_cflag = (CS8 | CREAD | CLOCAL | HUPCL );
That's line 117.
I got the RXTXComm source from http://rxtx.qbang.org/pub/rxtx/rxtx-2.1-7r2.zip. The Arduino app source that I modified was http://www.arduino.cc/files/avrdude-5.4-arduino-0010-src.tgz.
I made the same change in both places, just adding the "HUPCL" flag. This has the effect of automatically resetting the Boarduino when the serial port is closed so that it works the same way as the Windows Arduino app.