My harmony 550 always stops one input before the one I need on my TV. my tv has an input button that cycles thru all of the inputs. i've already checked that the inputs are listed properly on the setup page

On some TV's when you first press the input button it does not switch to the next input it just shows you the current input. It is the 2nd press that offten takes you to the next input in the list. This can cause problems with the Harmony. If your TV works this way then you will need to call Logitech and let them know about this issue. They can add the additional hit for you and then you can update your remote. If you are only using 2 inputs then A work around you can try is to tell the Harmony that there are more inputs, effectivly setting up Ghost inputs. You would put one ghost input after each input that you use. If there are 3 or more inputs then this trick will not work. The last work around is to remove unused inputs on your TV. Most TV will allow you to remove unused inputs. Then you can add one ghost input after each actual input: For example:
TV input1
Ghost1
DVD input2
Ghost2
VCR input 3
Ghost3

If I am missing some information just let me know.
I will do my best to help
Good Luck