Same thing for me... Everything worked fine with S01E01E02E03, and it does not work anymore with my Odroid setup + Jarvis (had Isengard on my previous setup)
See my post on kodi official forum Naming multiple episodes in one file
As very few people seem to use this feature, I decided to give it up and use MakeMKV to get one file per episode...
Sorry that does not help, but at least now you know you're not alone... 