Just to clarify I’m at the top of Middlesex county and have monitored this system for sometime with this issue just appearing the other day
Yeah, I understand. I don't think what you're experiencing has anything to do with whatever Skypilot is trying to claim is "normal".
It's been many years since I've touched a 780XLT, so I'm a bit rusty. The first thing I would try is setting the system to FM mode instead of NFM, see if that helps.
There is also the possibility that you're experiencing some local interference. I would scan all of the North Simulcast voice channels in conventional mode during a busy period on the system, and note how each frequency is being received. More to the point, make sure the scanner is actually stopping on all of the frequencies to begin with. In your video it appears that the scanner is skipping over 858.4625, which is one of the frequencies that sounds choppy when scanning in trunked mode.
Note that not all of the North Simulcast frequencies are used all that often (such as 851.5625 and 852.2375), so concentrate on the ones that are used most often:
856.4625
856.9625
857.4625
858.4625
859.4625
860.4625
Make sure that the scanner is stopping on all of those frequencies listed above in conventional mode with good audio. I would even suggest holding on each of them manually for a few minutes to make certain the audio is good. If you have any issues with choppy audio on any of those, then you're dealing with a likely interference issue more than anything else. Or, a bad repeater at the nearest subsite, perhaps.