I did some testing, results:
1. issue affects only the portable version (MC 16.x and 15.x, haven't used earlier versions), tested with Windows 11 Home, Windows 10 Home, Windows 10 Pro (user account only for the last one); Full installer version works ok with Windows 10/11 Home, didn't try with W10 Pro.
2. turning "Automatically re-sorts files..." on/off with applying, saving, restarting MC in different combinations doesn't help;
3. there is really strange behavior in portable; steps to reproduce:
Open a folder sorted by Name, with setting "Automatically re-sorts files..." checked on.
1. Rename file A to B.
The file does not move to its correct alphabetical position.
After refreshing the panel, the file immediately moves to the correct position (this step isn't necessary, just as a confirmation of alphabetical sorting).
2. Rename the same file B back to A.
Again, it does not move automatically.
3. Repeat the rename (A -> B) on the same file.
Now the file is repositioned automatically without requiring a refresh.
It appears that after the first renaming (A -> B -> A), Multi Commander "learns" how to update that file position correctly. MC "remembers" that file till you rename something else, then it "forgets" auto-sorting for the given file.