I think you're on the right track. Some sort of contamination in this system, especially if it's been a long time since it's been flushed.
Does it have an accumulator that you pressurized, with air or nitrogen, to keep this system pressurized? If that system lost pressure, or had some sort of contamination in it, it could have caused restriction at one of your control stations.
You may have succeeded in flushing the restriction out of that control station.
Doing a good flush of that system will give you the best chance of avoiding future problems.
I worked on control systems for over thirty years and figuring out what you have to do to maintain and keep them operational is always a challenge. And I don't have any specific experience on boat hydraulic systems. Just try to use common sense and figure out the best and easiest way to resolve the problem.