I found a possible reasoning and only partial answer! The problem lies in how s3d does things off the wizard vs NOT. I was having this problem and others after setting up just 2 profiles. After reading a bunch of threads similar to this one in substance, I decided to nuke my profiles and reload from the wizard. It magically worked! (well enough anyway that problems described here disappeared)
Even though it's exactly the same processes, s3d is somehow doing different linking of them when done through the wizard. And I think it seems to be PER MODEL setup. So if you get it once, you may have to start from scratch with the wizard and processes (normally I've just been using the same profiles then tweaking each time instead of reloading anything). When I redid from scratch, suddenly it stopped missing layers when it was only one color and properly printing the ooze shield before printing that color (still need to fix other retraction issues though).
So with your evolved problems, I believe that it's because s3d doesn't play nice with additional profiles thrown in and doesn't set it up to do proper order of operations.
There IS one suggestion I could give you if you need multiple processes though: try figuring out how to use the "group processes" feature for additional settings - or try using the wizard again? I think there's hidden code or a glitch making it so you need the wizard and/or grouping to make it properly work - and won't work even if it looks like it's fine if loaded differently!
Hope that works, I'll keep working on it, but I don't know that I'll get that far on mine for a while yet!