Let me take a crack at this. Though I don't think I have your answer.
The most important bit: A Next Actions view will never show a task if that task does not have a context that is currently open, unless "include closed" is checked in the "Filters" pane. The Next Action view will show more than one subtask, if more than one meets all the criteria to make the list, without regard to the parent task being a project or not.
With context times that don't overlap, only one of the tasks should ever show on Next Actions list at one time. If "complete subtasks in order" is checked, and the context is closed for the top task, then neither would show. You mentioned that it isn't checked, and you didn't mention a view in which neither showed, so this is probably not it. But the only thing I can think of with the information given is that perhaps "complete subtasks in order" is actually checked. It seems unlikely, but with the power of "Automatic Formatting" it could look like you have selected the parent task when in fact the properties panel on the right is showing you data for a subtask.
Extraneous junk to consider: I'm a fairly new user myself, and I've run into quite a few issues like this. The amount of time I've spent trying to figure out where I've made a mistake is very high. But I still believe MLO is going to save me time in the future, once I get all of these things right, so I chalk that time up to future productivity and consider it a capital expense. I don't know if that will help you, but it's what got me to go all in with MLO.
I also realized that I'm not going to be able to get many good answers to 'how my system works' from customer support or from this forum, because the flexibility of MLO gives me so many places to make a mistake and have a task fall through the cracks that it's nearly impossible to even explain the problem, let alone have someone figure out the answer for me.
So I have quite a few "safety net" views, with corresponding repeat tasks to check them, and whenever I don't understand why I missed something in the view I expected it to be in, I create another task to remind me to try to figure out why that is, and fix it.
So, in the past few months, I've re-designed my system about four times. But three of them were in the first couple of weeks, and one was recently. So I suspect that my workflow is getting closer to how I work, re-designs will become less frequent, and eventually (hopefully soon) it will be close enough that I'll decide a re-design is not worth the effort.
One tip I found useful: I use another checklist program or productivity app for some projects, and simply insert a task and a link in MLO. I do this when I haven't quite figured out how to make it perfect in MLO. I use Keep, Toodledo, and Evernote. for these few. But the number of tasks listed in those apps is shrinking and rapidly approaching zero.
So, I probably didn't answer your question here, but hopefully that info will help you decide to take the plunge and move to MLO.
My reason for deciding to take the plunge was that MLO seems to be designed to allow you to design a workflow however you wish, and when someone comes on the forum saying things should be changed in a particular way by the designers, the response is usually a polite version of "no, we like it configurable, not configured".
- Trevor.