From the probe itself, it may be a reference voltage that corresponds to a negative or positive doppler shift from the transmitted frequency. It may be the actual frequency differential between the Reference Freq and the returned signal.
There's more than one way to skin a cat and without knowing the specific piece of equipment and it's specs its pure speculation.
Thanks guys, this is useful. It's for a friend of mine who is dreaming about making his own head system out of a £200 netbook.
I'm guessing that what comes from the probe is pure analog signal, as from a microphone, and that the head system performs whatever signal analysis is needed to convert it into speed.