What you have described is what I expect, but not what I have observed. See here in this screenshot that the shadow track is rendering over the gameplay track, even though it is placed under it in the timeline.
I should also point out that I am able to recreate this behavior reliably; I’m not just in some corner case.
I’ll try to capture footage of me doing it.
You have filters applied to the video tracks. Although it shouldn’t, that might be causing this anomaly. Try applying the filters to the clips.
Look at the track blend modes. Default for tracks to behave properly is over.
I just re-created with a new project and no filters at all. Notice that this should have green (V3) on top; but black (V2) is the one that’s displaying.
That is most unusual. I put filters on the tracks and everything worked fine. Here’s a screenshot with all filters disabled. Yellow on the V3 is showing in the source viewer.
What version of SC are you using?
19.02.28.
This thread describes a situation where the top track does not render.
I just reproduced what the OP described. Removed track V2 then Undid it and now V3 is no longer rendering.
The way to fix it to remove the upper track and then add it back and put the clip on the track.
There is no undo in my use case. Here is a video of my problem.
Your video does not play.
It was just still processing on the youtube side. Try again.
Here’s another that repositions the clips just to be clear that all tracks are rendering, just in the wrong order.
I just duplicated the entire procedure in your video, step by step, and the upper track does not render. It’s probably because you insert the middle track. In my original project I created all 3 tracks before putting the color clips on them.
This might be a bug. I will upload my project.
Middle track bug.mlt (5.7 KB)
I removed the upper track then added it back and now the tracks render properly.
Thanks. I’m glad I’ve finally managed to convey what I’m experiencing.
I know I can do it by creating the tracks ahead of time. But it appears that render z-order reflects the order of addition, not the order of the clips in the timeline. So it’s impossible to insert a track underneath an existing track.
Assuming this is a bug, what’s the next step? Is there a way to report this? (I’ll try to find out myself; but I was thinking that bringing it up here in the first place would do that.)
It is a bug. One of the developers will eventually look at this thread and try and fix it. You can re-categorize this thread from Help/How to to Bug.
@Jonathon_Anderson, following your video method, I can confirm this is a bug, and works the same for me. I was trying to break it, but couldn’t figure out how to do it.
Using “Insert Track” or “Add Video Track” anywhere above V1, and below the top track will make this happen.
Using “Insert Track” or “Add Video Track” on the top most track works as it should, at least for me it does.
I opened https://github.com/mltframework/shotcut/issues/709 but I wasn’t able to say so yesterday because I hit the limit on the number of posts a new account is allowed to make. 
This is fixed for the next release v19.04.x
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