I assume the "drive you are working from" is an external. I wonder if that is the issue. I don't recall users complaining about this much of a slowdown.
What format is the file? I guess you don't say: is this dynamic link?
I assumed problems with scrolling down the timeline, but you mean a delay in Encore processing the new chapter marker, right?
Does it do it if the next chater is only 5 seconds down the timeline?
Does it do it with a short test segment? Create a 10 minute clip and see. If no slowdown, I'd conclude performance. If the slowdown is still there it doesn't rule it out.
But if the problem is present with the short clip, copy it to the laptop internal drive, create a test project, import there, and see if you have the problem. That may be the best workaround.
You might try a workaround