I'm not sure that I follow your focusing technique fully..
I'm guessing that you want to use hyper-focal techniques, but your description isn't exactly that..
With new lenses that are not inscribed as the old ones were, it isn't quite as easy as it used to be.. But, you still don't just "focus in mid-way and have the whole image in focus". Hyper-focal focusing is based on the the idea that depth of field typically extends 2/3 behind the point focused on and 1/3 in front, and varies based on aperture. With older lenses, you calculated your hyper-focal distance and the f-stop needed, then rotated the lens focus barrel so the infinity mark rested on that f number, and then everything from infinity back to the opposite inscribed f number would be in focus.. (or, of course, you focused on an object at your calculated distance) See, if you just focus halfway, or what seems like halfway, then you may have things in focus at a hyper-focal distance (2/3 behind the focus point and 1/3 in front) but you don't actually have that calculated distance in front of you, and so your "in focus far point" may be short of that distant object - your lighthouse. - You didn't focus on a point out far enough to capture it.
So, ask yourself... am I focusing so that my infinity mark is further around the lens barrel than it might be if it was inscribed (for DOF) similar to the old ones ? For it to be accurate, then your infinity mark HAS to be at a value that does not exceed where the value of the (non-inscribed) f-stop is. If you actually calculated your hyperfocas distance, then that distance would be the number that is at the lens center mark when you have focused.
Here is my 2 cents.. 1. I think that you are enlarging the distant subject (pixel peeping?) so much that you see it at it's worst. and, 2. I believe that you are concerning yourself with getting the foreground in focus and not really nailing the distance objects (You need to bring the infinity mark back in towards the lens center line a bit more and to within the "range" of your chosen f-stop) ..