It is related to:
#1294

Although the issue above is fixed by pull request #1506, there is a small glitch.
In spi_com.c, compute_disable_delay(), spi disable delay is calculated by:

disable_delay = ((prescaler * 1000000) / spi_freq) / 2;

if the spi clock > 1MHz, i.e. spi_freq / prescaler > 1000000, disable_delay is 0, which actually make this fix invalid.

The solution shall be:

disable_delay = ((prescaler * 1000000) / spi_freq) / 2 + 1;

It was tested to work on our environment.