I have literally just setup the same service on whatbox.ca as you have. But am not having the issues you seem to be. But, then I do run some post processing scripts after download before the file hits the rclone cache remote.
The only difference I can see if that I have a longer --cache-tmp-wait value to you. Because Plex will scan and analyze the media file after its moved to the rclone cache location I tend to leave the file there for a few hours. I have recently increased this value to 12 hours as I have some users who will watch a new movie as soon as it hits Plex and to save API and Transfer requests for a recently uploaded movie, I opt to keep it local to the server for a little while. Seems to work nicely for me.
(Also, I would advise against posting your google oAUTH ID, Password and Plex Token on forums)