Hi,
szangvil:
Any ideas why I had to change the baud rate?
Because the bootloader, fuse settings, and crystal (or resonator) establish that the baud rate has to be 115200.
Is the baud rate settings used by avrdude are for the PC-FTDI chip communication...
No. The PC and FTDI chip communicate via USB at a USB bitrate: 1.5, 12, or 480 Mbit/s (probably 12).
...or the FTDI-ATMEGA chip communication?
Yes.