File types shouldn’t matter but the support article is listing a number of prerequisites/conditions, e.g.
- not all clients will be able to play stacked files
- files must contain the same tracks in the same sequence
To verify if the files are properly stacked, check if the runtime in Plex is the full length of all stacked files.
If Plex recognizes that the files were previously associated as different versions, doing a Plex Dance might fix this.