Have you tried a rescan on your box? A rescan may help tune in all channels.
If this fails, please let me know and we can troubleshoot more.
After looking at the equiptment, Willis is correct, If you are using a MYSKY HDi Box to get the Free Channels (Without a Free TV Subscription) will be unable to get the HD Versions of 1,2,3 Prime, TVNZ Duke and more. You will need to contact SKY in this instance and ask to have these channels however they may charge you.
You will need to get a Freeview via Satellite box to get all the Freeview Channels without a paywall.
There is no workaround with the MySky HDI box,
Willis that seems right, it says HD after the names of the channels. Is there any way to get the non HD version?