Not sure of the reasons. If I use one to start and another to end, it does generally have an effect. I don't use the phone app much, easier to use the remote. I suspect its somewhere along the lines of the Harmony "toggle" command.
FIrst, the actual remote used should make absolutely no difference- the commands are the same and it should work the same as if multiple people were receiving messages using Morse Code- the dots, dashes and spaces should mean the same to everyone and whether the code used is IR or hexadecimal, it should work from any controller when there's no two-way communication, like Sonos, etc that shows a change of state in the remote. As far as the 'Harmony toggle command', that's not Harmony's command, it's up to the IR control chip being used and/or the product manufacturer. If the discrete Harmony ON/OFF commands don't work, it's because the device doesn't use them or they were disabled.
The equpment manufacturers don't generally make IR control chips but some have a solid state devices division (Toshiba, Sanyo, etc).
I installed an extensive system for a customer and after a couple of years, they decided they wanted surevillance cameras, so I installed those, with a DVR in the same rack. To make it easy to see what was happening outside without going to the computer or using a phone/tablet that may not be in the family room, I decided to send the video to the TV's component input since the DVR didn't have HDMI and the AVR's component inputs were already being used. I added the needed commands to the activities (Harmony 1000 or 1100, don't remember which but it wouldn't matter) and when I pressed the DVR's Menu button, it switched to the wrong TV input and locked the TV's setup. I had installed a Pioneer commercial plasma, so it had no tuner, but the setup could be locked in applications where someone messing with it would cause major problems for a venue.
I had to scramble to get the info for unlocking the setup (this happened at 3PM on a Friday afternoon) and after getting the system to work normally again, I called Harmony to find out what happened. Tech support, which was as good or better than anyone in the industry as far as remote code maintenance, analysis, etc, saw the code in the customer's account, but asked me to learn an input code- they said the problem was caused by both companies using a Toshiba IR control chip and then, explained that these come from the chip maker with a fairly long list of commands with assigned numbers, but no name, so they could assign that for their own uses. What may be 'Command Lock' for one brand might be called 'Input 3' or 'Menu' for another. If the device manufacturers want to disable commands, they can.
Time Warner and other cable boxes have been another thorn in our sides, for decades- Only toggling power commands work and for awhile, a 'power-numeric' command could be used, but they disabled that, too. I called Scientific Atlanta to find out if discrete power commands could be used and was told that as they were sent to Time Warner, they had that ability but it was disabled. Those boxes also had an IR input jack on the rear and that was also disabled. Anyone who had tried to get an IR emitter to stick to the concave lens knows why that jack would have been very helpful.
I don't know why discrete commands are disabled, but it tells me that the manufacturers don't care about ease of use for people who buy these or those who have to program remotes and deal with all of the setup problems. Having discrete commands would have saved a lot of money for a lot of end users and prevented a lot of headaches for installers (their own, too).
