I understand all this..
I am using usb-uirt with girder - there's no option to change the length of codes there.
When I use any remote (but harmony) and watch girder log - it works perfectly. ut of my many remotes i found that aiwa sends the shortest and simplest codes.
So, I went to harmony setup and used an aiwa device as a template for htpc. worked but as with other remotes in harmony database it would do some unpredictable things.
I also reprogrammed a universal remote to aiwa cd player and tried to teach harmony those codes - again, almost success, but not 100% - main issue - when I press a button it sends a different code depending on the length of the press. So, I have to press several times before the right code goes out.
And you're right it only happens with the PC (uirt/girder). All audio/video components work perfectly with Harmony