Hello! I don't use anything like that. All I have is the Thrustmaster Warthog HOTAS stick/throttle combo and a cheap Thrustmaster pedal.
I doubt anything's "wrong" with your peripherals. The "stock" GNS systems work flawlessly.
What I suspect (without any basis to state it, only guessing) to be the problem is that Nick somehow managed to solve the issue of the RNAV system not being able to drive the autopilot. Back in the MSFS 2020 days, this ILS tracking issue didn't exist, at least I didn't experience it. Since the RNAV system of Black Square aircraft is now capable of working with the autopilot, the problem appeared. At least, that is what I suspect. But I may be perfectly wrong. It just makes sense to me that while Nick managed to somehow workaround whatever prohibited the RNAV system from coupling to the autopilot, the solution to one problem might have caused a different problem.
Whatever is causing the problem, I hope Nick can find a solution.