Originally Posted by Beerstalker
I have heard that you can go to your dispay device and delete all of the inputs except the one you are using and it will stop issuing the input switching commands. I have never tried this so I am not positive though.
Actually, I did this but instead of deleting all the inputs except the one I was using, I deleted ALL the inputs for that device. Basically, once you go into the Logitech Harmony software go into "Devices"==>"Settings" for the particular device, i.e. "TV"==>"Advanced setup for this device". Just hit next for the next few options until you get to the screen that gives you a list of all the input names like "HDMI, S-Video, Component, etc.." Once here, delete all of them so the box is now empty of inputs. Click next until you're done. From what I've seen this "tricks" the remote to bypassing a reconfirm of that input. This has worked perfectly for me.
Thanks Beerstalker for the tip and thanks to the original poster for his solution aswell.
Hope that little write-up helps others.