I struck the same problem - here is what I did to work around the problem: this applies to the Harmony One
The key problems to address are that (i) the Oppo 103 has a slow startup from cold; (ii) the Oppo forgets its last input setting when shut down.
At the step in Harmony wizard setup which asks "What input does your Oppo 103 need to be on?", instead of selecting "HDMI In-back" you instead select "Source in put is missing" button. The next screen shows 4 options - use option number 4 which is to emulate a Toshiba TV. The next screen shows the various inputs of the Oppo 103. Be aware that these Oppo103/105 inputs can be selected by number as follows:
#1 Bluray Player
#2 HDMI / MHL in-Front
#3 HDMI In-Back
However nothing to select on this screen - instead move to next screen: "Select the remote buttons to press to display source input, and to confirm source input selection":
In this screen use the drop down menus for
"Remote button displays source input menu" ==> "Input" ;
" Source Inputs" list (shows the above list) ==> leave these as is;
" Remote Buttons" ==> use drop down menus to input numbers 1,2,3, etc per the above list.
"Remote button confirms the source input" ==> use drop down menu to show "Select" (this is probably unnecessary, but does not hurt).
Then carry on thru the next pages which basically confirm you settings, and save.
Having described all this, I now advise that I abandoned the approach because you also have to adjust time delays for the various activity steps to allow for slow startup of the Oppo (and other equipment) or else not all of the Harmony steps are received at appropriate times when cold-starting the overall system....there is no problem (with delays) for controlling the AV system via the Harmony once everything is started, just at restarts. I had the system operating okay as above until the last firmware update when something changed(?).
Anyway, I did not want to again go and fool around with programming key-stroke delays once again, but instead went to a 2-step sequence:
Step one I named as "Start System" : using the wizard I just set this to start up all needed equipment and have all (except the Oppo) select necessary inputs or outputs, etc. No sweat.
At the Oppo settings screen I selected "I dont need to set the input on my Oppo 103". This leaves the Oppo displaying the "Home Screen" after system startup.
All the other programmed activities like "Watch TV", Play DVD", etc. where the Oppo may participate, I just used the necessary input selection on the normal page "What input does your Oppo 103 need to be on?". That would be "HDMI In-Back" in your case for WATCH TV activity.
This works for me because I do not press any activity button on the Harmony (to select an actual viewing activity) until after the whole system is started and whatever input selection signal the Harmony sends to the Oppo will be timely & appropriate.
Thank you for the detailed explanation. I ended up doing what you described as the 2 step process after I could not figure out how to make everything automated. As you said, I figured out that once everything is on the commands work as expected. So when starting the system I just press "Watch a Movie" which boots up the TV, AVR, and Oppo. Once there I just press "Watch TV" and the DVR boots up and the Oppo automatically selects the "HDMI In-Back" input. I think this is the easiest thing to do. It's only 2 button presses and is much easier than going through the pain of setting up a macro with delays and such. This 103 is a beast. I set the sharpness to +1 for my Cox Cable box that I have running through the HDMI input in the back, and it made a world of difference to my eyes. Cleaned up all the fuzziness of the cable feed without introducing jaggies. I think it definitely worth it running the cable box through the Oppo even if you have to jump through a couple hoops. Others may disagree but I have been pleased with just turning up the sharpness to +1 and leaving everything else at default.