Same with mine. Seems to be the way SuperMicro does it for whatever reason.
Also, sometimes missing slots still take a number. might only have slots 2, 4, and 7 for example, the others just don’t exist.
you know looking at the diagram would help a lot, you’re right I had it set wrong wow, this simple error has been bugging me for over a week, I really need to look closer at the diagram
the top slot is 7, and the next x16 slot is slot 5