limor:
you can tell avrdude directly to toogle a line before uploading. I expllained it here http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1187984620/12#12 and used it in a makfile wich is linked.
you simply add a section like this to $ARUINO_DIR/tools/avr/etc/avrdude.conf:
programmer
id = "arduino";
desc = "Arduino Serial Bootloader";
type = stk500;
reset = 7;
;
In the avrdude.conf is a SUB-D RS-232 connector pin mapping which shows RTS is pin 7 (hence reset = 7).
Well, after seeing this again, I may have done something wrong, as I initially wanted to toogle DTR (which is pin 4!) but it worked with the setting above!
I've to look at the board again - I probably soldered the wire to one FTDI pin aside or something 
...
But it should work in general, as it toggles a reset on my trusty Arduino Extreme/USB boards.
Or maybe the reset does come allways from the general serial port opening? I'm too lazy now to pull my scope from the shelf...
Mellis, what did you find out with avrdude and reset?
p.s. to use this new avrdude option, preferences.txt (or the makefile 
must read upload.programmer=arduino of course