Please help with Sky,STRDA2400ES, & Harmony One.

OK. I just upgraded my amp to the Sony STRDA2400ES. My TV is a JVC LT-32DY8ZJ. I am using the Logitech Harmony One Remote.
I'm trying to set up the activity to 'Watch Sky'. Here is my problem..... The TV, and Sky come on as required, then the Amp switches to the SAT channel, but then the TV flicks back over to the AV5 input.

This is how the activity is setup.....
http://www.avforums.com/forums/attachment.php?attachmentid=106974&d=1233249996
The Sky is connected to the TV via a SCART cable. The Sky is connected to the AMP via an Optical Cable. The AMP is connected to the TV via an HDMI cable (but I dont think this is relevent)

InputVideo 1 is the right channel, because I can manually select it with the TV remote and watch as normal. SAT is right because the sound plays as normal. Help please...

 

You've answered your own question - it's the Scart causing the problem, one that often arises!
Change to a better connection, to a Scart that isn't fully wired, or to Scart adaptors with 1 video and 2 audio cables.

 

I was gonna change from scart to component for the sky box, so I can run the video through the amp and use the upscaling thing.

 

Yes, that should give you a double advantage - any three core cable with RF plugs will do.
Hope that's helped but let us know if there are any other problems or questions.