I've mentioned problems with the system before, but when multiple layered backgrounds are used in the same scene, Naninovel ignores the layer ordering and puts them in what seems to be an almost random order. (example: I order one as Front and one as Back and the Back appears in front of the Front).
Using multiple backgrounds is necessary in situations where you need to offset something in the background, since it's impossible to offset a single layer in a background.
We've seen this problem over and over again in all of our projects, and the workarounds tend to be very complicated, such as changing some actors to characters just to force ordering. It would be good if all enabled backgrounds were processed at the same time and all layers sorted properly before rendering.

As one example, I changed everything possible between two layered backgrounds (Layer of prefab to UI vs. default, layer of sprites to front vs. back, different z values). No matter what I do , it always places one background at 99.9 and the other at 100 in the scene and the wrong one is always in the back.

No issues on my end using the latest 1.18. Be aware that to sort the background actors on a z-axis, you need to use the third value in pos or position (https://naninovel.com/api/#back) and when none is specified they will be defaulted to the values specified in Z Offset and Z Step options in the Backgrounds configuration, which is 100 and 0.1 by default (the latter option will cause the second background to be placed 0.1 points in front of the other background in order to avoid z-fighting aka flickering, hence 99.9)

If you're still having issues or you're referring to something else then we'll need a repro to investigate this: https://naninovel.com/support/#reproduction-project