You must make sure the inputs configured in the harmony software EXACTLY match the inputs on your TV - same number of inputs in the same order (names don't matter). Check this under the TV device, Adjust Inputs.

Also - the first time you use the activity you must use the HELP button to sync the inputs if they don't work immediately. Help allows the remote to keep track of where it is in the list of inputs. If you manually fix it by using the source button (on the OEM remote or the 550) then the remote software thinks it's correct and will continue to choose the wrong input.

Once you verify the input lists match and you're using the right commands and you've used HELP to synchronize it the first time - it should work fine. If it comes up short (doesn't send enough source commands) try increasing the inter-device delay.