Wow, a lot of good information! Several times you said you had not added the phase coupler because it wasn't needed. Most of the problems you mentioned would probably go away if you add the phase coupler.
When you do a signal strength test from Upstart what numbers do you get? What size house is this in?
The UPB signal can travel thousands of feet, out to the transformer on the pole and come back. With the phase coupler the signal take the shortcut and is much stronger.
About 3 months ago I installed over 80 UPB devices in an 8,000sqft home with very great success. The owners are thrilled with local (by room) and global (whole house) scenes, all work every time (no call backs)
There are many programming options in Upstart that may not be obvious at first. Just because it doesn't work right away, It probably is a missed setting in the UPstart programming. There is a learning curve there.
In reference to the light requiring 2 button presses... If you have set the control button to a toggle it will send an on, on the first press and an off on the second press and an on, on the third, etc. If you turned the light on with the button and then off with an "all off" or other scene, the "toggle" button will not know that and you will need to press it twice.
I decided to use "link activate" or "link deactivate" on the control panels and make each button a "scene" , That way you will get what you want every time you press the button. I would only use a toggle if that were the only button controlling the device or link.
I installed SA 1 rocker 4 button switches in every major room for local scene control and an 8 button at every major entrance to the home and in the kitchen and master bedroom. As an example at the entrance from the garage I programmed the buttons as follows. Buttons 1-4 control outside functions; Garage lights on, Driveway lights on, Gate open(single press)Gate close(double tap), Garden lights on. Buttons 5-8 control inside scenes; Party scene, Evening scene, Pathway to the master bedroom/with kitchen, and All off.
As mentioned above you could purchase the HAI control switches and assign the button indicators to scenes(links) and they would indicate what scene you had activated from other locations.
By the way the house operates without a main controller, I added a PCS timer module for various timers.
If you have questions on UPB call Simply Automated or Powerline Control Systems(PCS)
Dave