Thanks Mark.
I think I've accounted for that, though, I've left the CS unaffected when using the Due functions but have driven it low and high when testing it with the old code (only when #define FastSPI has been commented out)
For example, in my code I have sections like this:
#ifdef FastSPI
SPI.transfer(TFT_CS, index); // Using the Due SPI function without affecting CS
#else
digitalWrite(TFT_CS, LOW); // Drive CS low
SPI.transfer(index); // Old school SPI function
digitalWrite(TFT_CS, HIGH); // Drive CS high
#endif
Cheers,
Dax