I hate being the bad guy but someone has to start the discussion.
Unfortunately, I fear this is a system failure that is common in the kit log house industry. We, here on this forum all have one thing in common... we are all building a non-kit log home to avoid several of the problems that you have inherited.
Before we see more photos I'll take a stab at your home's problem.
1... Your "logs" have been milled on the tops and bottoms where they rest on each other. The horizontal joints are flat, fitting tightly together. Any water that finds a way to that joint sucks itself in as far as it can and tries to stay there. It then promotes fungus that promotes decay.
Test this theory by putting a 2x4 flat on top of another board in the weather. Within weeks you'll see the fungus growing between the boards.
2... Your roof overhangs are not long enough to prevent rain water soaking the walls. This is not a problem for a normal stick framed house because the walls are water resistant.
It is a serious problem for a home built with the boards (referring back to the flat on flat scenario in point 1) that have a potential water sucking inlet every 6" as the rain runs down the wall. You could spend two lifetimes recaulking and resealing every exterior crack, but the house is made of wood and it wants to twist, shift, and breath. I think you are correct that the "stain" is not helping the problem but I suspect that removing it will not solve it.
Gutters are not enough. Longer roof overhangs or a complete wraparound porch is what it takes to keep the logs dry. This is exhasperate by the deck that fits tightly against the wall.
Take a good look at this LHBA website and you'll quickly see that your problem is totally what we lifetime LHBA members are all here to avoid. Personally, my home has a minimum 6' roof overhang on all sides and my logs are all naturally round with no flat surfaces for water to suck into.
I am sorry that I don't know the solution. I do know that it is perhaps the commonest problem in the kit house industry and you are definitely not alone. Google "kit house rotten logs".
PS... My feet are in the hammock that is suspended from the rafters some 6 feet from the log wall.
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