So, the first upload works because everything on JKSV's side is local and a mirror of what is happening based upon response codes from the server.
What you're describing afterwards indicates JKSV is failing to get a listing at boot. It fails to create the folder because it already exists, but can't see it. When it constructs the URL, it's missing the parent ID, and it just uploads it to the root.
I'll see what's up with it later if I can.
@TheGioGrande
I think I got it.
I'm running Apache and its responses always have a trailing '/' when dealing with directories. Forget that. I'm working on it now. It is really odd though. I'll get back to you once I have it figured out. It's really bizarre, actually.