Here's a few things for you to consider:
- The "duct junction box" is properly called a "plenum". And if you measured on the cold side of the air handler, it's called a "supply plenum".
- Air does not mix equally within a plenum like this. Every cooling coil has what is known as "coil bypass factor". This is air passing through the cooling coil that does not drop in temperature or humidity, or at least to the levels we want for air conditioning comfort.
- What you may be measuring in your short and long run ducting is a combination of thermal stratification, radiant heat gain, and uneven mixing of air in the supply plenum. Without taking a lot more measurements all over the attic, this is my educated estimation of what's going on.
And yes, before anyone asks, air in motion can thermally stratify. Meaning you can have moving air within a duct at one temperature at a lower level, and another temperature at a higher level, or vice versa. The first time I ever measured this and figured out what it was, I was blown away, pardon the pun.