I have same problem, when downoading TV series that still releases the new episodes every week. New folder is created with (1) or (2) at the beginning of the folder name. I have to delete this and then Tixati says that the folder already exist and I simply click ok.
Episodes that I watched I just turn off at the downloading window.
I tired of deleting it every time. Is there any option to download the torrent to same folder if folder is already exist without adding these (1) (2) etc.