Sounds like your box is working in single cable mode. To check go into the Setup menu. Press Red, Green, Yellow, Blue, Green, Yellow, Blue in succession.
In the menu that comes up Check Antenna Setting says - Fixed and Connection type is - Two Cables(Same).
If incorrect make a note of your recording schedule and either do a factory reset or change the connection type in the above menu.
On the reset you should see a two cables found message.
Check two tuner operation by starting an instant recording on BBC1-HD, start a second on BBC-HD. Check you can view and live pause any other channel.