This has everything to do with the way that Kodi scans files in, as it looks at the FolderModifiedTime to figure out whether or not to scan it for new items. Usually when you add files to a folder it will change the modtime but, for some reason, rclone is unable to update this property when you upload folders.
See this thread for information and the workaround until mtime is built into the software. There are a few issues open on github but I’m unsure when/if it will ever get addressed… I hardly understand @ncw’s last comment on the issue- I know that they are words but not what they mean in that order.
Please be advised that library scans will take for-fucking-ever in Kodi if you change the fast-hash setting because it will literally scan EVERY FILE to see if anything has changed, rather than looking at a folder’s mtime and updating only that folder if mtime>last scan time.