freeduino serial v2 'not in sync'

Initially I had trouble getting uploading to work on the command line in linux, but eventually got that all sorted out. Now I am getting the following error:

robind@Vlad ~/robotank $ make upload
perl pulse.pl
/usr/bin/avrdude -V -F -C /etc/avrdude.conf -p atmega168 -P /dev/tts/0 -c stk500v1 -b 19200 -U flash:w:applet/Blink.hex
avrdude: stk500_getsync(): not in sync: resp=0xf0
avrdude: stk500_recv(): programmer is not responding
make: *** [upload] Error 1

The pulse.pl script was the key to making it work in the beginning. It simply toggles dtr to reset the board: Device::SerialPort->new("/dev/ttyS0")->pulse_dtr_on(100);

I'm running gentoo linux, using a straight through db9 cable. LED 13 flicks once on a reset, and flick 2-3 times when i run pulse.pl. It also flicks additional times when I try to upload. Uploading was working fine before, I'm not sure what's changed. Any suggestions?

Tried the parallel port programmer on the off chance that would fix it. However, I couldn't get that to work either. Avrdude says "device not responding".
I don't understand why it's not working. The flicking LED on the board indicates the boot loader is still intact. I've read that rx/tx pins can be indicators of whether the board is still working or not. If I put some leds on those, what kind of blinking should I be looking for?

I've got a Duemilanove that experiences that problem if I try to upload a sketch via USB while also running a BlueSMIRF bluetooth radio off of the protoshield. If I remove the bluetooth radio module I can upload the sketch without any problem. Once uploaded I can power-off and reattach the bluetooth radio.

I will double check to make sure I don't have any applications running that might be affecting my serial port. However, I'm not convinced this is the problem as I get the same error under Linux, where I am positive I don't have any software running that would do that.

If you have multiple serial devices on the board itself you might get the same problem on any OS. I had it with XP/Vista and OS X before removing the extra serial device form the board.

It can be the atmega168 chip or the bootloader on it. Was the board working or it gave the same error from the beginning?

duncan: these errors happen with nothing plugged into the board other than the db9 serial cable to my pc and 9v.

nkcelectronics: The board worked before. I was under the impression that because led 13 flicks normally, and flicks when I try to upload that the bootloader was intact. Is this not so?