Thanks for responding and for your input, I answer your questions below,
>You're transmitting a 250kHz square source which is the summation of all odd harmonics of >250kHz. I believe that is why you were told to switch over to a sine wave which you would >probably just see a single tone.
I have switched over to a sine wave, but I still don't get the single peak on the FFT as one would expect, that's the source of this conversation.
>I am sorry if I am unfamiliar, but what exactly are you trying to
>accomplish, and how do you expect to do it with a square wave?
What I want to do (for now) is be able to correctly digitise a signal and write it to file (thereafter I will do various signal processing). My short term objective is to digitise "off air FM signals" and perform ambiguity measurements.
I'm using the sine wave as input and plotting it's FFT to see if I was able to correctly digitise it. This should be a fairly trivial 5min process but I've been at it for a week!!
Thus far non of the suggestions have helped cure my problem.