Thank you Clark for the push – I had another look around and discovered that both 0×0D (13) and 0×0A (10) were being received by the AVR. Linux was adding the extra 0×0D in front of my 0×0A, causing all the data in the command buffer to be shifted down one, which resulted in the changed numbers, and the strange text output. After a bit of searching, I found that the stty utility can be used to turn this feature off:
stty -F /dev/ttyS0 -onlcr
So that’s that – now I can get back to working on a utility to encode some colour bitmaps to store in the remaining 10K on the ATMEGA168 I’m using 