Hi Ryan, are you using the mayaUSD proxy shape or the standin to load the usd files ? (the way it needs to be built and packaged depends on that)
In any case, I need to warn you that apart from the complexity to build everything properly, you'd be jumping several major versions, the current head of the arnold-usd repo is being used and tested against an Arnold 7.x that hasn't even been released yet. If you're in production, such a huge jump could introduce many more issues.
That being said, what you need to do is to build the procedural, following the build instructions in https://github.com/Autodesk/arnold-usd/blob/master/docs/building.md . You can't build just the translator portion of the repo, you need to go at the root and build it as described. Basically you need the build variable BUILD_PROCEDURAL enabled and you can turn off all the other BUILD_x variables that are for the render delegate, etc... If you're building it for mayaUSD then you also need to set a variable USD_PROCEDURAL_NAME='usd_cache' .Then you'll get either a usd_proc.dll or a usd_cache.dll that you need to copy to the right location, depending on whether this is for the standin or mayaUSD proxy shape.
On the other hand, there's a chance we could help you workaround the problem if changing the usd scenes is a viable option. This randomness was caused by a very specific use case, where an instance points "directly" to a file reference. If it was pointing to e.g. a Xform node in the scene, which has a reference just below its hierarchy, then this randomness should disappear. So if you're ok to share example scenes with us, feel free to contact us at support@arnoldrenderer.com and maybe we can find a way to tweak the scenes in a way that doesn't cause the issue. I would personally think it would be much better if you're in production, but of course it's your choice.
Cheers