Upon further inspection, it seems like it is fine when there is a 4.1GB directory by it's self. Once I add a 200GB file it stops syncing, uses a high cpu amount, and starts reporting "Don't have permissions to write to the selected folder." on both directories after a couple of minutes of scanning, and appears to have stopped scanning the large 200GB folder after 6.6GB. Also, after reading the logs, it seems that the issue is "ReadFromDisk: Too many open files"