Software changes and evolves over time - if nothing ever changed there would be no reason for updates would there ? Sometimes those changes may have unintended side effects in specific circumstances that may call for a change in configuration.
The repeat delay (delay until repeating starts when a button is held down) in OSMC was reduced in an update a few months ago - from memory it is about 0.75 seconds now, while it was nearly 2 seconds before that. It was reduced due to many requests from users to reduce it as it was taking “too long” before it started to repeat. (I also found it too slow to start repeating before the change)
If a quick press of the button on your remote keeps sending an IR code for more than 0.75 seconds (which 3 repeats on a harmony may well do) then it will cause unintended repeats - that’s not our fault, and the only thing we could do would be to increase the delay to be very long again - but that disadvantages everyone whose remote controls work properly…
The problem here is that the harmony keeps sending the IR code for much longer than you actually press the button - and this is fairly unique to the harmony remotes, as the vast majority of standard remotes stop sending the IR code the instant that you release the button.
I know this because I have a Harmony One myself and have spent many many hours programming it and trying to resolve these exact types of issues on other hardware other than Raspberry Pi’s running OSMC…and have spent plenty of time trawling the Logitech forums looking for solutions too…
There is an advancedsettings.xml setting in Kodi that you can increase the delay before repeats begin, this is called remotedelay:
http://kodi.wiki/view/Advancedsettings.xml#remotedelay
The default is 3 which means after the initial press Kodi will ignore the next 3 repeats sent from the remote before Kodi recognises a repeat. Try setting it to 20 which should definitely solve your problem, then gradually reduce it until you are happy with the result.