It depends on the motherboard - some SKIP PCI-E slot ID numbers when assigning them to certain slots even if you're using all of the slots.

There's also a well-known issue where the DRIVER doesn't always assign the "id number" of the card in the same order as the PCI-E identifiers - both in Windows AND in LINUX - that affects all multi-GPU miners I've worked with, a couple even have gone so far as to come up with a "work-around" to MAKE the displayed miner numbers line up.