Its always the little things that trip you up, having checked my "hidden files" (which happens to be a lot) i found 7 "rtorrent.rc" files with various ~ . and - in and around them, which i can say i dont understand. Ive now only got one and i reinstalled rtorrent and it now has my settings working so thanks again 666.
In the explanation of how to use the author uses a: ^ to mean control. How do you input the options which dont need control pressed first for example:
u
Display transfering blocks.
and,
I
Toggle whether torrent ignores ratio settings.
Are these options done with enter/return?
Sometimes when i get frustrated with linux id love to just go back to windows but something stops me mainly my common sense!

So excuse my earlier comment it was down to ignorance which was bliss while i was with windows!
