Generally, if two pickups are constructed the same way with the same resistance they're going to sound similar to one another in the same guitar. My understanding is that the construction of the '59 hasn't really changed much in production in quite a long time - so your pickups should be built the same way unless there's some defect, and it's a good sign that they measure the same resistance. There are a lot of Chinese knock-offs out there, but if you bought direct from SD you should be good on that front.
So that suggests a difference between the guitars or electronics themselves. Make sure that you've measured distance from pickup to strings on both guitars - pickup height can change the sound and feel of a pick up a good deal. Then double check the actual measured value of pots (it's not uncommon for potentiometers to be +/- 20%, which will make an audible difference). The amount/type of wire that you use to do hookups inside the guitar itself can also add capacitance - if one guitar has longer runs than another then it will tend to sound darker. Then, as mentioned, strings and wood of the actual guitar can factor into things as well. I guess that it's also possible the quieter humbucker somehow became degaussed. Maybe it got stuck next to a really powerful magnet at some point or something?