Are you using a blue focusing filter? If so, don't.
I did a series of experiments some years ago in which I got the probable erors of focusing with a grain focuser with three different filters and none. There was a focus shift on the average in one direction with blue, the other direction with red, and none with white or green light. The cause was the chromatic aberration of the eye. Also, the standasr error of focus was greater for both red and blue focusing filters than it was for green or no filter. You can be as scrupulous as you want about the 1/2 mm or so of paper thickness, but the random errors of focus swamped that out. These results were in Darkroom and Creative Camera Techniques, now Photo Techniques.
No matter what printing filter you use, the focusing should be done by the light that the eye sees best, which is green or white.
The effects of chromatic aberration of the eye are well know to astronomers, where they show up as apparent chromatic aberration of the telescope.