I just had the same problem, go to Configuration -> Channel/EPG -> Channels. Make sure each channel not showing up has a Channel tag.
If you want you can go to the Tags tab and make a custom one.
Now go to Configuration ->Users, now edit the User that you are using on the front end.
Scroll to the bottom and in the drop down window labeled channel tags select all your tags. Click Apply
Now on the same window click "exclude" channel tags, Click Apply, and now Un-Click "exclude" channel tags.
This seems to reset something with the user settings. Refresh your PVR front end and the channels should show up.