I have a Harmony 550 wit a Samsung 4061. With this TV, I must press source to shuffle through the various inputs. The problem is that the remote consistently picks the wrong source. For instance, I choose Watch TV as an activity and the source chosen will be for watching DVD. Did anyone else have a similar problem? And do you remember what you did to fix it?

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.

Check the device Adjust Inputs configuration. The default for the Samsung Model LN-T4061 is the discrete method (Method 2). If you are using the default discrete method, then check the behaviour of each input command in device mode, then make the necessary correction(s). If you have to use the cycling method (Method 1), then, as Akirby said, make sure the list of inputs is the same, in the correct order and you answered all the questions correctly.

Also, remember that Samsung TV's skip inputs which are not used. This is selectable in the Harmony software. Air or antenna input is always active though. If all else fails you can use a programmable remote such as a one-for-all remote to program the advanced or discrete codes for the specific inputs the learn them into the Harmony. This is a more robust solution.

Ultrav23, are you saying that the One-For-All remote contains discrete commands that are not already in the Harmony database?
Note 1: If the original OEM remote has discrete commands (or any other missing commands), then you can teach them directly to the Harmony remote.
Note 2: Sure the discrete method is more robust, but the device must support discrete commands. The Harmony database may contains discrete commands for a brand but not all models (for that brand) support discrete commands. That is why one should try all the commands in device mode to see if this particular model supports any of the available discrete commands.