i didnt buy a long HDMI cable because i thought that:
they were expensive
lost signal over long distances.
However, the amount I spent on a hdmi extender and two cat 6 cables 25m in length was probably the same as a 25m HDMI cable in the end. I hope the signal is good - i havent checked the picture quality as i dont have a tv attached to my onkyo yet.
I will take your advice, and leave the hdmi Cat6e extender on at all times (this looks to have resolved the problem)