Change SPI clock polarity between a WRITE and a READ instruction

Hi - I was on holiday last week, hence the lack of replies.

While it's unlikely to be your problem, you'd want to remove integer= from your code, as that's not doing what you expect :)

SPI.setup might be resetting pin states to their default values which would throw things off - you could try a slightly hacky method of just updating the software SPI values directly:

var spi = new SPI();
spi.setup({sck:B6, miso:A6, mosi:A7, mode:integer=0, order:'msb'});
digitalWrite(SS, 0);
spi.write(0b01000100);
spi._options.mode=3;
d = spi.write(0b01000100);
digitalWrite(SS, 1);

Otherwise I'd say to just manually create the waveform using for loops and digitalWrite. Some kind of oscilloscope would probably really help you do see what's going on though.