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Can you try reducing the bit rate and check if you still face this issue?
Looks like there were few elements in the RX FIFO that were not read during the previous transaction (0xDB 0xFB 0x46) and that this were read during the next transaction. Maybe that is why you see these 3 bytes of data and then your actual data.
Can you please provide a more clear waveform image of the transaction? (With clear markings of which is MISO, MOSI, CLK and SS)?
The SPI Done Interrupt (AFE_SPIM_IntHandler) is only triggered every 4 ms. But it should trigger every 2ms, because the sampling rate is set to 500 SPS. The timing diagram below shows the problem.
The SPI Done Interrupt is triggered whenever all the elements in the TX FIFO is transferred. I do not understand what you mean by "should trigger every 2 ms because data rate is 500 SPS"? Could you please provide more detail?
Can you please share your entire Creator project file (zipped version), so that I will try to reproduce your issue at my end?