and they don't seem to care at all.
Are you this negative in real life or just online? With the attitude you're giving towards the developers in this thread and in all your others, it's no wonder you're not having people jumping at trying to help you. And to say "they don't seem to care at all", have you not noticed @Luke has replied 10 times in this thread?
I'm running 3 instances of Emby right now with 3 different versions. I primarily use the latest beta for media conversion, but tried it on both other versions as well after seeing your issue. Emby cleans up the folders every time on ALL versions. @sluggo45 is also seeing no leftover folders. In fact, this is the only thread on here that I can remember seeing with this issue. You say you're a programmer so you should grasp this concept.... if there's 1 user out of tens of thousands with an issue in a widely used feature, is it a bug in the software or is it related to the single user with the issue? It's not impossible that it's a bug that only 1 user has experienced, but odds are good that it's something in that 1 user's configuration that's causing the issue.
It sounds to me like a permissions issue as well. You said it yourself that you SSH into your system to change the permissions to be able to delete the directories manually. That should be your proof that this is related to permissions! I'll leave it to you to figure it out though because I've got better things to do than try to help someone that will turn around and say I don't care or I'm blowing smoke up your ass.