Your explanation about the weights you have makes perfect sense. My machine only came with the large + small (it's a few years old so perhaps they tweaked the package - you get less for more!).
Based on the wording in the manual, I would guess that if you have all three weights attached, 55 lbs is not a valid reference tension. In other words, the markings on the "yard stick" are only valid from 68-81 lbs.
Doesn't explain the OP's observations though