I think the issue ( if there is one ) is one of trying to fit a quart into a pint pot.
I tie myself up in knots by insisting on working on small layouts. To do so, there are compromises needed. This is exactly the same.
I still feel that the goods shed is causing the problem, even the small wooden job.
Personally, as mentioned in my earlier post ( but following further pondering ) , I'd either straighten the goods shed road and move to a position 'opposite' the station building,
OR
Straighten the goods shed road and shorten the road behind the goods shed which would allow the goods shed to be set back a bit.
Another observation is that looking at the wooden goods shed, I think the dimensions are not helping. Sorry, Larry but I think it's too tall and the area where it's out is above the door/ window. Take out three planks, lowering the roof and I think the look of the whole structure improves.
In a confined space, I work on the basis that having tall structures will cause the scene to look compressed and crowded. I think this is contributing to to making things look ' not quite right ' .
I feel a more squat profile for the goods shed would alleviate this.
Rob