First, I would suggest you check out the first thread in this section, Harmony Slow Response. Most likely your lag issues can be fixed by adjusting your delay and repeat values.
Second, there is an enter button on the lower right side of the 659 next to the zero button. I would check to make sure that it is programmed as enter. However, if your original TV remote doesn't have an enter button, I doubt there will be one available for the Harmony, and if there is it might not work.
Third, have you tried 3 channel numbers to change channels. Sometimes by entering three numbers it will change faster. So for channel 9 enter 009, or 035 for channel 35.
I think that most of your problems with the Harmony can be solved pretty easily if you do a little more homework. However, it could be the fact that your remote is a refurb, and it might not be working correctly.
I wish you luck, and I hope you can get your issues solved. I know that I have become very happy with my Harmony remotes, as are everyone else who uses them at my house.