This issue is driving me nuts. I am working on a project with some other guys who built the electronics. We have custom boards with an atmega 1284p. For USB cummunication with the 1284p we use a FTDI FT230X USB Bridge (http://www.ftdichip.com/Products/ICs/FT230X.html). This doesn't hav DTR. RTS is used to reset the board using a capacitor (pretty much like with off the shelf arduinos). The arduino bootloader is used, and we use https://github.com/maniacbug/mighty-1284p to upload. The board selected is "Original Mighty 1284p 8MHz". After installing the right ftdi drivers from http://www.ftdichip.com/Drivers/VCP.htm I can upload to the board from a mac. Linux has these drivers built into the kernel. However, I cannot upload to the board. AVR gives the following error:
avrdude: ser_recv(): programmer is not responding avrdude: stk500_recv(): programmer is not responding avrdude: stk500_getsync() attempt 5 of 10: not in sync: resp=0x00 avrdude: Send: 0  
dmesg gives the following:
... [ 51.299964] usbcore: registered new interface driver ftdi_sio [ 51.300088] ftdi_sio 1-1.2:1.0: FTDI USB Serial Device converter detected ...
... Bus 001 Device 006: ID 0403:6015 Future Technology Devices International, Ltd Bridge(I2C/SPI/UART/FIFO) ...
The settings for the mac and linux machine are identical. On both I use arduino 1.0.5. Both do see the correct serial port.
I've seen many posts in this forum with similar problems, but have yet to find one with a solution that works for me. Holding reset, or clicking it just before uploading does not work. As suggested in some forums I have tried with removing brltty to no avail. I have tried uploading with the arduino IDE, eclipse with avr plugin and avr via commandline. None will work. I've tried it on different maachines as well with different versions of ubuntu, and uploading works in none of them. Adding -c arduino to avrdude command doesn't do the trick either. Any ideas on how to fix this?
P.S. Programming other arduino types, like a duemilanove work fine under linux