Which boooader did you burn to the MCU and via what method?
The bootloader has a baud rate it expects communication on, and this is complemented by the same rate set in boards.txt so the IDE knows what baud rate to use when invoking avrdude.
If you use Arduino as ISP to burn the bootloader then you normally do it with a target board selected and hence the correct bootloader and boards.txt entry are in sync.
If you used a different method to burn a bootloader file directly then maybe the bootloader and boards.txt entry don't reflect each other?