Harmony Remote & LG 55LM6200 Issue?( help please very frustrated)

[zodiak]

guys

I have a Harmony 1100 which I had setup for over 4 years, I recently added a 3D tv( LG LM6200) and a sony BDP S790 an in doing so I added these devices to my harmony 1100.

How this should work( my setup)
I have a Pioneer elite 03 receiver with a Sony PS3, Motorola Cable box,
Sony S790 BD player.
The setup:
PS3 using HDMI into the Pioneer
Motorola using HDMI into the pioneer
Sony S790 with dual HDMI outs( HDMI 1 out to tv, HDMI 2 out to pioneer-this is the suggested use of the HDMI outs HDMI2 was labeld audio)

Now my problem.......

When I use the Harmony and chsoe activities the LG's INPUT LIST appears and the correct HDMI port is not always selected other times it is and most all the time the INPUT LIST screen stays on the screen for many seconds if not minutes.
There should be a seemless transition from one device to the next, however there is not.
Im very frustrated at this point I cant seem to get this figured out, what I think I know is that:
1-When in the Logitech Harmony "Device Setup" I dont know how to select the way this remote selects inputs,
it wants to know how the "original remote" selects inputs I dont have the original what I have for a remote is an LG universal AKB73615315 remote, on this remote I have a INPUT button on the top of the remote, one press brings up the INPUT LIST, from here I can either continue to press the INPUT button (which cycles through only the inputs I have in use, ie HDMI 1, HDMI 2 or I can press the direction arrow and this will cycle me through all the available INPUT possibilitys-which if I pressed the ok button would take me to that INPUT even though its not connected to any device just an empty output source, example TV or COMPONET) so Im not sure whats the correct choice when being asked how do you inputs with original remote.

Second this LG 55LM6200 has a feature called "simplink" which Im not sure what it does, what I think I know is that if I dont have HDMI 2 set to this simplink when I chose Bluray on my harmony as an activity, the TV will not select HDMI 2 as is programmed.
However if I leave the simplink on, when I try to leave the Bluray activity and go back to cable or game, the HDMI source stays on HDMI2!!!

I have no idea how to configure this or if there is some compatability issue here, no matter how I try to configure this I seem to always get the INPUT LIST when I select a different activity.

I know the harmony works fine, I know if I had this run from my receiver to the TV with just on HDMI from Pioneer to the LG I'd have no issue, however again with my needs (pioneer isnt 3D capable, I need to use this dual HDMI output from the BD player- here is my issue Im certain.
Is the issue how Im setting this up? or some thing else please help if you can

Im to the point where Im certain its something Im missing or not selecting correctly but Im at my wits end please help