Ok thanks for the replies, I'll work on getting the start logs. But your right Squid, Sonarr definitely won't move a file thats currently in use by seeding. I've been thinking about ways to get around this, like having an extractor extract and make copies of the mkv file to another folder that had the same container path as sonarr. Sonarr would then see just that file and not a rar'd archive that is seeding. However I'm not sure that's how this all works.
In the end I might just subscribe to using nzb files, seems like a much more popular choice!
Thanks again for the reply!