Bob. I used to have the exact same problem on my planes.
Now, they looked perfect with the naked eye, but with the long stick trick I could get the high rates to match exactly.... but when I set the AFR and dual rate (futaba 9Z) I could not get them to match perfectly. I could get them close, to within 1/8" on an 18" long stick but not exact. I measured and remeasured pushrod lengths and control horn settings with a vernier caliper and they were exact. But the darn throws would not match up. As you said, I could go back and adjust for low rates, but then the high rate would not match. More head banging[:@]. I never really figured that out. I just accepted that 1/8" at 18" om low rates was just EXTREMLY close to perfect and dealt with it. Since I started programming, that became a non issue..

I just dont know and never figured out exactly what the problem was. Was it a servo resolution thing? Was it something to do with using subtrim? The ATV's were the same,,,, I just dont know? IF you figure it out tell me. That is what drove me to programmable servos. I have gotten pretty doggone good at setting up matched deflections mechanically, and what I considered imperfect some may have considered spot on, I dunno.

That slight difference seemed to make no difference on low rates for precision flying, but it made a big difference if I left the offset on the high rate. It would cause lots of problems like dropping a wing in a wall, hard to manage waterfalls, wingrock in harriers. Stuff like that so I always perfected the high rate.