And Ctein's method of determining the actual focus relative to the paper position is simple and reliable. To me, the main question here is "are the grain focusers giving accurate focus on the paper?"; and this can be clearly answered with a few sheets of paper using his method. Then if things are off, at least you have some solid footing to work from in figuring out the problem.
I don't want to open a can of worms but I believe there could be an error of focus with respect to ultraviolet vs visible in my system... which is quite different than the norm (though not an unreasonable system). I use graded paper and an Aristo grid bulb through a Xenar lens... I may have a system that is more susceptible to focus errors due to ultraviolet exposure than the more common tungsten sources used with multigrade paper through an APO lens.
Our Original Poster here, though, seems to have something very unusual going on, a gross error that really sounds like tampering, dropping, or possibly a bowed piece of paper.
Peak 1 in conjunction with an enlarger will measure smaller distances than a consumer grade caliper.
In terms of focusing on the paper or the baseboard, I don't have an opinion on the matter, just the optical formula that predicts about a 2mm focus spread at f2.8 at 9x enlargement. This easily encompasses any photographic paper or film of which I am aware.
Modular transfer function focusing equation (equation #38 in http://www.largeformatphotography.in...DoFinDepth.pdf) :
N_max ~ 20 / (1 + m) sqrt(dv)
N-max = F number
m = magnification
dv = focusing leeway on the baseboard
20 = constant for circle of confusion about 0.15mm on the print
I think our enlargers are built the wrong way round!
They should have the light source, negative and lens at the bottom, projecting upwards onto a piece of ground glass for focussing which is then replaced by a paper holder for exposing in the same way as the ground glass and film in an LF camera.
Then we could check the focus with a loupe or even just our eyes without casting a shadow.
Steve, on a large table/baseboard that means bending over the groundglass, maybe leaning even on it...
I'm the killjoy again.. But actually I like that idea!