Spent quite a bit of time in trying dozens of possible solutions to my problem with my remote controller then today while I was messing around with my settings I came across IR Blaster which  I thought I had not seen before. Tried setting it up but wouldn't work. Checked cable and found the usb was not fully seated in TV so pressed it home and set up IR blaster and Hey Presto the Sony remote controller works perfectly including channel changing.

If at first you don't succeed try and try again!

It might be an idea to include IR Blaster issues among the possible causes of remote controller not working properly.