Hi Debbie
The V6 remote shouldn't need unpairing, but remove the batteries from it so it can't connect to the 360 box.
Make sure that the 360 box is connected to the internet (by ethernet cable if possible)
Also try new batteries in the 360 remote and make sure you've pulled the plastic tab off on the back of the 360 remote.
How did you pair/re-pair the remote? Did you use the correct 'Live TV' button? (the one on the right hand side directly below the red power/standby button)
It should work by holding down the 'Live TV' and '0' button together for around 10/15 seconds. The Standby button should then start to flash followed by an onscreen message displaying 'Pairing successful - this remote will only work with this Virgin 360 box'.
You can also try the following:-
Put the box into 'Pairing Mode' by pressing the Standby/On button on the right hand front of the 360 box for 10 seconds. Then using the remote control, press and hold the 'Live TV' button and the '0' button together for 10/15 seconds. And fingers crossed hopefully a message should appear on the screen confirming that pairing was successful.