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See this line in SPI.cpp
spcmd0 &= !(((uint32_t)0xFF) << 2); should be spcmd0 &= ~(((uint32_t)0xFF) << 2);
spcmd0 &= !(((uint32_t)0xFF) << 2);
spcmd0 &= ~(((uint32_t)0xFF) << 2);
The logical not makes the mask 0 and wipes out the earlier settings. Should be a bitwise not to make the mask FFFFFC03.