Possible error in UC3 framework AT32UC3A-1.4.0 and older:
definition for AVR32_SPI1_NPCS_3_0_PIN is missing although there should be four such pins on the SPI1 peripheral.
Another observation regarding SPI on the EVK1100 kit:
If you use only one of the NPCS-pins ranging from 1 to 3 in SPI master mode, remember to check the state of the NPCS0 pin although you don't use it for SPI. That pin is connected to a SPI mode fault detection circuit that looks for other SPI masters in the system trying to select the UC3 as slave.
A solution is to simply switch off the fault detection in the SPI mode register or include NPCS0 pin in the GPIO setup for SPI.