Just a quick question:
From the waveform you sent it looks like the SPI_CLK(DPI3) signal starts from a LOW state. Do you have pull down on SPI_CLK (DPI3) pin?. If yes, could you please remove the pull down and either leave the DPI3 signals floating or connect a pull up and check if the problem persists?
The reason why I mention this is because the reset configuration of SPI port for SPI master boot is CLKPL=1 which means that the SPICLK signal should be HIGH when idle.
Message was edited by: Mitesh Moonat