I'm using a similar setup and am having the same issue as OP. As soon as the LNM webserver is stopped the tick/stutter in MSFS stops.
Completely disabling LNC and Flow on the MSFS host doesn't change anything.
Before finding this thread I had a theory that perhaps LNC and LNM polling MSFS at the same time was causing the tick. I tried feeding LNM on the MSFS host PC via it's LNC feed instead of directly from MSFS, but that changed nothing.