i am using an ATMEGA 1284 with the mighty-Boatloader (GitHub - maniacbug/mighty-1284p: Mighty 1284P Platform for Arduino) and the standard ftdi-chip (ft232). It is not possible for me to upload a sketch via the ftdi-chip, I always get the "not-in-sync" error. I use a 0.1uF Capacitor between DTR and Reset and a 10k Pullup on the ATMEGA reset pin.
When i change the processor to an ATMEGA 328p everthing works great. Also uploading sketches to the 1284 with an isp is no problem.
Today i worked on this error and I reduced it to the following strange behaviour:
When I upload the Bootloader via my AVR MK2 and directly after that upload a sketch via the FTDI, it works! But when i upload any sketch via the AVR MK2 (Upload using Programmer) , there is no chance to upload a sketch after that with the FTDI. The only think you can do, to get the FTDI-Upload working ist to reflash the bootloader.
When you select Upload Using Programmer (MKii) the bootloader is overwritten with the sketch, so FTDI uploads will not work as there is no longer a bootloader.