Serial Over USB Reading With GNU Octave Problems
I have solved the problem, so I will post the answer. It was indeed a timing problem. To repair the above program, I actually removed the delay in between the command "x" and the read. I cannot say for sure why the program would not behave properly with this delay, but the best way to get the data was to remove it: send the command, read immediately, send the stop command, delay. 

Thanks for the help @Chris Stratton. Although the problem was a smaller one than expected!

Sam