Since upgrading I have noticed that Tixati chooses to pick files to download within the torrent. It seems based on size? and occasionally I have to pick through the files and add the necessary files to the download. I have noticed that it also leaves the larger files outside the torrent folder.

Is there a way to turn this 'feature' off and leave the file structure and content as it came?

settings->transfers->files and disable always auto-select files in new transfers

You could look there first ...