I rang back, the system was slow so the lady couldn't get into my mothers account so she's going to ring back. She said the 3 way calling hadn't been taken off and she'll deal with that when the system allows her to.
The 'TW 1MB SAVING' is a discount for having all 3 services, so we get £4.00 off the bill each month! So as chrisjones stated, the initial request for 3 way calling to be removed and credited back has been ignored but they've knocked 4 quid off the bill each month.
Anyway, she did ring back and said she'd taken the 3 way calling off the bill and credited back the £12.19, so hopefully this really is case closed! But we'll wait until next months bill shall we