A single sample of our i.MX6Q custom boards has an intermittent boot up issue:
When pressing the i.MX6 reset button (or on POR), the i.MX6 sometimes (~20%) fails to generate SD3_CLK to read the boot partition of the eMMC (on SD3). In this situation, the i.MX6 enters serial download mode instead of booting from the eMMC.
Once in the serial download mode, I have verified the DDR3 SDRAM passes cal and stress test.
The 32kHz and 24MHz clocks look good.
For debug, I have forced the i.MX6 to use its internal ring oscillator, instead of the external 32kHz crystal ... and booting is still intermittent.