I have a brand new install of virgin V6, install was done Tuesday 7th Feb. On the 8th the remote started showing exactly what you have, intermittently not working. I called in on the 9th to support and they re-paired for me. Worked until the 11th when it again intermittently stopped working for several minutes. The TV functions (volume, mute, on/off) still works. I called in to support again who said they're sending a new remote out, should be with me in another 3-5 days.
And like you using the app from a android device works absolutely fine. The remote also seems to work fine whilst in the netflix or Youtube app I have not seen it not working whilst in either. But as soon as I've come out of either app the remote has sometimes stopped for a few minutes.
gently squeezing the bottom sides of the remote, next to clear and Last Ch , it then works during that intermittent issue. I release the squeeze and it stops working. Squeeze and then works. until the intermittent issue goes away at least and it works for a while as normal again....for a while.
This is good to know!! I had the old TiVo remote programmed to also turn off power on a power strip, which was lost with the new RF remote. By switching this function off I can again control power to the peripherals from the remote now.