Have you installed a bootloader on your homemade version?
The odds are stacked against you trying to use a 12 Mhz resonator. The serial communication driven by the bootloader is dependant on the clock frequency of the 328. To get it to work at 12 Mhz, you'd need to reprogram the bootloader. The chip will happily run at 12 Mhz, but you can't expect timing critical operations like serial to work without recoding the bootloader.