Make.md file hierarchy not working as expected

What I’m trying to do

I am using Obsidian on a Windows 11 system.
I installed Make.MD in Obsidian, and created a space, made quite a few notes properly structured. Something like this:

Base Folder A
→ Folder B
    → File A
    → File B
→ Folder C
    → File C
    → File D
and so on…

Then, on next day, when I opened Obsidian, in the MakeMD navigation, these files were no longer in these order, even though they were stored correctly, by the navigation of Make.md tab was all messed up. Something like

Base Folder A
→ Folder B
→ Folder C
Folder B
File A
File B
Folder C
File C
File D
and so on…

Basically, all files and folders came out to the root level and there was no proper hierarchy, although it was maintained exactly the way I had created in the file system, the files and hierarchy shown in the make.md tab was all messed up.

How do I fix this?

Hopefully someone can answer here, but you may have better luck in their Discord server. There’s a link to it on their home page: https://www.make.md/.