Harmony Remotes - Programming

[FWgirl]

We just bought a Sharp Led Tv that is connected to the U-Verse Motorola system and a Bose Lifestyle System.  I did all the set-up as instructed, but have a weird glitch.  If all the systems are off, when pushing the "Watch TV" button, all systems come on, but the U-Verse system flickers on and off on the TV and the "HD" light on the U-Verse also flickers on and off.  The only solution is to disconnect the power source to the U-Verse and let it re-boot.    I am wondering if I need to put a delay in the remote for turning on the U-Verse.  On our old system, when the TV came on, the screen would say "Push OK to turn on U-Verse".  I don't ever see this with the new set-up with the Harmony Remote.

The other glitch happen after the TV has been on for a couple of hours.  The remote will no longer change channels or the volumn.  The screen on the remote asks if all systems are off and to push help.  However, when turning off the systems with the remote, nothing happens and after using the help prompts numerous times, I finally get all the systems off. 

Any help would be appreciated!!!