Hi awneil -
According to the data sheet sec 188.8.131.52, what you are seeing is expected behavior.
If you want to send multiple bytes with the SS asserted throughout then you should disable the Master Slave Select Enable and you will have to handle the SS line manually.
probably not what you wanted to hear... i know the spi peripherals in other Atmel parts allow hardware control to send multiple bytes without wiggling the SS line between each byte.
Discussions around product based on ARM Cortex M0+ core.
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