Setup:
Panasonic 60ST60 - HDMI 2 (ARC) input
Sony CT660 Soundbar - HDMI ARC [labeled as the "TV" input on the CT660] (to panasonic TV) / HDMI 1 (from HR44 stb) / HDMI 2 (from xbox)
DirecTV HR44 - HDMI out (to CT660)
XBOX 360 - HDMI out (to CT660)

Settings: Panasonic Viera Link ON / Power On Link=NO/ Power Off Link=NO/ Automatic Input Switching=OFF
Settings : Sony CT660 HDMI control=ON

Was having problems switching activities using the harmony ultimate with this setup. System was occasionaly cycling through too many/too few inputs and not ending on the correct one. I was set on keeping the ARC feature since my wiring is already setup for the 1 HDMI cable running from the wall mounted TV to the soundbar and also the ability for ARC to pass-through better audio than optical. I want to use my sound bar as the switcher.

Primary issue was the CT660 soundbar ending on the incorrect input for the activities I had involving smart TV features. these include "Watch Netflix" and "Start DLNA server". I could not disable the Automatic input switching between this soundbar and TV for any SMART functions on the panasonic. I had the ultimate set to power on TV, power on CT660, set TV to HDMI2, and set CT660 to either input 1, 2 or TV(depending on activity) to no avail.

Here is the fix: in the harmony remote settings, change the settings on any smart TV activity to "do not set input" on the soundbar device. This way, when you begin any of those activites (ie. netflix button on the panasonic, DLNA server on the panasonic, Amazon+, etc) the soundbar will not try to cycle through the inputs AFTER the soundbar has automatically switched to "TV" when it detects a signal from a TV App.

Lets say i then want to exit back to the directTV on the HDMI1 or Xbox on HDMI2, I just start that activity and it powers back on the device. (note: this is no problem for me since the HR44 is directv's newest box and is almost instantaneous in turning on). I would be interested to see if this causes too long a delay for slower cable/sat boxes.

let me know if anyone has any comments or issues, but this seems to work for me so far without connecting an optical cable or making things too slow with crazy delay settings.

I would suggest that you turn off all CEC settings when using a Harmony remote. The Harmony sets up the Activities, and required commands, based upon the basic commands. The CEC functions only confuse the command sequences.

The CEC functions are primarily for OEM remotes for equipment from the same manufacturer. Again, these features will only confuse the Harmony activity.