Ethernet controller is sometimes not listed in lspci

I am using a CPU Board PCE-3029G2-00A1E from Advantech and I am facing an issue. Sometimes (not always) one of my ethernet controller is not detected by the system (not listed by lspci command). This card have 2 ethernet port and the one which is sometime not detected is always the same. Initially, I have faced this issue on QNX 6.5 SP1 system but I am able to reproduce it on a linux distro (puppy linux 9.5, I don't tested other linux distro.). The result of lspci | grep "Ethernet" (the missing one is 03:00.0):

00:1f.6 Ethernet controller: Intel Corporation Ethernet Connection (2) I219-V (rev 31)
03:00.0 Ethernet controller: Intel Corporation I211 Gigabit Network Connection (rev 03)

I specify that it seems to happen only if I do a cold boot. If the 2 ethernet controllers are detected, a reboot does not seem able to reveal the problem. Also, If the problem appears, a reboot seems to not be able to fix it.
Do you have any advice to help me to know if it's a problem due to hardware, driver or maybe such of initialization time?