Very frustrating and I can't explain why you have experienced what you have and if it's any consolation to you it would seem that none of us, me included, can give an explanation that resolves the issue. Bob-D659 has really covered all the likely issues but if none of these apply then I am stumped.
I have two Paterson grain focusers. The micro and the major which is much taller for large prints. It avoids bending down over the print while trying to adjust the focus. There is a very marginal difference between the two so minor differences may not be unusual but not ones that show up on a print that I can see although I should add that my biggest print is 8x10
However as your best print is the eyeballed one then it may be that your best bet is is to obtain a Kaiser focuser or the Nova Darkroom one called I think a Hocus-Focus or some such comical name. Others here who have got one may know the correct term.
Both work on the principle of simply magnifying the projected print instead of focussing on the grain. I have the Kaiser as well and I find that it does as good a job as the Paterson if you find a line that demarcates light from dark such as a window frame. Both will also do their jobs into the corners of the projected image
Before selling all your grain focusers however just make sure there isn't an explanation and solution that you have overlooked. It'd be a pity to sell all your grain focusers only to find that there was a solution.
Best of luck and I hope someone can suggest an answer