Firstly I'm not sure what "everything minus Sky" actually means in package terms, but all the same.
Can you confirm - for the avoidance of doubt - that CatchUp programmes from ITV, C4 or C5 are also affected by this "not included in your package" error? Anything else is potentially not included in certain TV bundles, those are - so it would be useful to be clear.
You've mentioned that another box in your home is working fine, the next obvious thing is to swap the boxes around and prove whether this is a box-specific issue. It's still not necessarily a fault (depending on the answers to my other points) but it's something else to test one way or the other.
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I think I can shed some light on this issue as I have extensively tested out why it was working on one V6 box and not the other We have two TV's and two set top boxes. Iplayer stopped working on the box upstairs. No problem, swap the boxes over. Strangely the boxes behaved the same way. The box I moved upstairs is not working for iplayer, but the one I moved downstairs is working. The downstairs TV is LG. The one upstairs is Samsung. I Put the boxes back on their original TV. Now I get the monitor off my computer and plug that into the Box upstairs that originally could not get the Iplayer. Now the iplayer works. It seems to be a problem with the samsung TV so I reset the TV to factory defaults. Still cannot get iplayer
Along the way I tested the boxes and TV's on different cables and in different places. It is DEFINITELY, for me, a problem with Samsung TV and happened when I switched over to the Beta version of iplayer and back again +I looked online to see if Samsung TV's have a problem with iplayer and it turns out that iplayer queries the TV for a certificate of some sort, but if the certificate is out of date the TV is unauthorised to use the iplayer.
Get your computer monitor or a different make of TV (NOT SAMSUNG), plug it into the box see if that works
I've just added something to my post on the issue of Amazon Prime/YouTube not working for me. I haven't tried other services but it would be interesting to see what your boxes say.
I've found that when this happens, going into "System Info" on the box, on the second page under "HDMI Status", it shows either "Not connected" or "HDCP not enabled". When it's working OK, it says "HDCP 2.2 enabled".
Again, this is on a 4K set and wasn't a problem more than 2 weeks ago.