HiLuckyB
I have my 2080 TI in the top PCI slot, And my Titan X Pascal in the 4th slot. Programs like EVGA Precision and MSI afterburner read the Titan as GPU 1 and the 2080 TI as GPU 2. I ran these cards like this in my X99 FTW K with no problem's, But on the X299 Dark it's Reversed.
 
Most of the time this is not a problem, But there are a handful of game's including Metro Exodus trying to use the Titan And not my 2080 TI 

I've seen this happen before when I was running SLI or running with a dedicated PhysX GPU. I've never had it cause an issue with game trying to use the other GPU though. It is an issue with how the devices are enumerated during boot by both the hardware and the OS.  About the only way you might be able to resolve this is a complete reinstall of the OS with only your GTX 2080 Ti installed and after performing a cold reset of the BIOS by removing the battery for 15 minutes after resetting the CMOS. Reinstall the battery and go from there with a clean OS install. If you have a spare drive, you can test this out without blowing up your existing OS install.

HiLuckyB
I have my 2080 TI in the top PCI slot, And my Titan X Pascal in the 4th slot. Programs like EVGA Precision and MSI afterburner read the Titan as GPU 1 and the 2080 TI as GPU 2. I ran these cards like this in my X99 FTW K with no problem's, But on the X299 Dark it's Reversed.
 
Most of the time this is not a problem, But there are a handful of game's including Metro Exodus trying to use the Titan And not my 2080 TI 

Make sure you have your monitor cable plugged into the 2080 ti, and not the titan.

sparetimepc

HiLuckyB
I have my 2080 TI in the top PCI slot, And my Titan X Pascal in the 4th slot. Programs like EVGA Precision and MSI afterburner read the Titan as GPU 1 and the 2080 TI as GPU 2. I ran these cards like this in my X99 FTW K with no problem's, But on the X299 Dark it's Reversed.
 
Most of the time this is not a problem, But there are a handful of game's including Metro Exodus trying to use the Titan And not my 2080 TI 

This is actually normal in pretty much all of the X299 series boards that i know of, mine does it as well with 2 different makes and models of X299's.  Doing a clean install will make no difference Whats confusing is when using the classy tool with kingpins, one software PX1 shows them in reverse order and classy tool shows them in correct order. 

Correct. Just doing a clean install with the same hardware setup will give you the same results. You actually have to remove the hardware and let the motherboard renumerate it. I've been able to solve it on two motherboards, the third would not put them in the correct order no matter what I did.