If that's the case, then its probably just your delays - especially your power-on and input delays. Take a stopwatch to the input change and power-on of your TV (your cell phone probably has one) and then add half a second for good measure and you're usually in good shape - you can tweak in 500 ms increments from there.

Do note that the Harmony will send every discrete command to every device in an activitity when you change activities as opposed to the bare minimum of commands.

Most devices are happy with an inter-device delay of around 100-200 ms, which may speed things up a little more. (Or a lot more given your 3500 ms entry right now.)