SPI fails to read first 6 bytes - stm32

Question

I'm having a lot of issues with SPI module on my STM32F051 MCU. I've got it configured as a master to drive a slave flash memory module (that doesn't really matter).
I'm trying to read 8 bytes from memory, this is how the 'read data' message is structured:
First 4 bytes of the message are transmitted, next 8 are received.
First byte is 'read data' opcode, three following are data address and equal 0 in this case.
Code:
memset(out, 0x00, 256);
memset(in, 0x00, 256);
out[0] = OPCODE_READ;
out[1] = 0x00;
out[2] = 0x00;
out[3] = 0x00;
uint32_t len = 4 + size; // size == 8
spi_select(M25P80);
HAL_SPI_TransmitReceive(&hspi1, out, in, len, TIMEOUT);
delay_ms(BYTE_SPEED_MS * 5); // Needed because ^ finishes before physically
// transmitting the data. Nevermind the 5, it
// was picked experimentally
spi_deselect(M25P80);
Signal (yellow - clock, red - miso):
At 488 bits/s transmitting 4 bytes takes 4 * 1E3 / (488 / 8) = 65.5 ms. Then the reception starts. Memory starts transmitting [0xFF...0xFF] right away, but contents of the 'in' buffer are:
[0x00 0x00 0x00 0x00] [0x00 0x00 0x00 0x00 0x00] 0xFF 0xFF 0x00...0x00
^ zero because this ^ should be 0xFF ^ correct data
is the part where
data was being sent
to the memory
So first six bytes of data are just lost. Am I the only one who's having such a hard time with STM's SPI module?
EDIT:
I've gotten myself a different eval board with a slightly different MCU (STM32F030) and it gets even weirder:
[0x02 0x02 0x02 0x02]
0x00 0x02 0x00 0x00 0xFF 0x00 0xFF 0xFF 0xFF 0xFF 0xFF 0xFF 0xFF 0xFF 0xFF 0xFF 0x00...0x00
Although I must mention that I'm using a different compiler with this MCU.
EDIT 2:
The way I partially got it to work is using 16-bit mode with SPI. This fixed this particular bug, but there are more similar oddities with STM32's SPI.
EDIT 3:
SPI initialisation code:
void MX_SPI1_Init(void)
{
hspi1.Instance = SPI1;
hspi1.Init.Mode = SPI_MODE_MASTER;
hspi1.Init.Direction = SPI_DIRECTION_2LINES;
hspi1.Init.DataSize = SPI_DATASIZE_16BIT;
hspi1.Init.CLKPolarity = SPI_POLARITY_LOW;
hspi1.Init.CLKPhase = SPI_PHASE_1EDGE;
hspi1.Init.NSS = SPI_NSS_SOFT;
hspi1.Init.BaudRatePrescaler = SPI_BAUDRATEPRESCALER_2;
hspi1.Init.FirstBit = SPI_FIRSTBIT_MSB;
hspi1.Init.TIMode = SPI_TIMODE_DISABLED;
hspi1.Init.CRCCalculation = SPI_CRCCALCULATION_DISABLED;
hspi1.Init.NSSPMode = SPI_NSS_PULSE_DISABLED;
HAL_SPI_Init(&hspi1);
}

Answer 1

Are you sure that the initialization of SPI is right?
Maybe your Clock polarity or phase settings does not match between Master and Slave?
Take a watch to ClockSettings.
Please show your SPI-Initialization-Code!