First off, I'm deliberately referencing this question and have read both the original question and every answer, and I just wanna make sure to note that I know how to focus manually and am in fact moving the focus ring.
I recently bought not one but two old Nikon 50mm f1.8 Series E lenses. One of them is the newer variant, one is the older one (see also this page for visuals). I first purchased the newer model, but then realised that the aperture blades are oily, and because I found another lens very cheap, I also bought the older model and that one does not suffer from oil on the blades.
I own a Nikon D3300 which does not use a split-image prism and is generally not recommended for manual focusing. Nikon DSLR's -- even those cheaps ones -- do have a focus dot in the viewfinder which can be used even with old manual focus lenses. Having said this, here's my problem:
Using the 'newer' Series E on my Nikon D3300, I get sharp images when the focus dot indicates the image is in focus (The dot is visible and does not flicker). See this image:
However, on the older Series E, I get completely blurry images when the focus dot indicates the image should be in focus. (See the following crop, taken at F1.8, 1/2500th, ISO 200)
I've double and triple checked that I indeed set the focus pixes to the middle element and have tried to account for every kind of user error I could think of. Lastly, I have used the Live-View to focus manually and the images that I get from that are certainly sharper (see following photo) than using the focus pixel. They are not as sharp as possible, just serve to illustrate the issue. Additionally, when I use Live-View to focus, switch back to the main viewfinder, the focus dot is not visible, indicating the camera does not think the image is in focus.
How can this be? There are no electronic contacts between camera and lens, so the focus dot should work 'optically' and should not care what lens is in front of it. I've tested this on another Nikon DSLR and the same result happened there, too.