How are you determining that the strings have different tension? Is that a "feel" thing based on plucking? Is it am amplitude thing? Have you stuck a strain gauge on there? Not trying to be a jerk, just curious about the unit of measure and how quantitative vs. qualitative it is.
In theory, the tension of a string set to vibrate at a specific frequency depends on the length of the scale and the density of the string - which for basses usually means the string diameter and the type of string (round vs. flat wound? Metal type, core type etc.) So, if the strings are the same type, same gauge, same material, same manufacturing process (i.e. the same) and the nut and bridge are set up properly so that they are acting as proper anchors, then the only difference that could cause a difference in string tension is the scale.
This argument applies to playing an open string. If you are playing the e-string, at the 3rd fret and observing a difference in tension, it could be related to the fret or string height and the repeatability of the your finger position between two different necks. Seems to me that would be pretty subtle though.
I've been able to feel the difference in string tension (at the tuning machines) when tuning a 30" scale bass vs. a 34". Not sure I could tell the difference between a 0.100 string and a 0.105 on the same bass. You may be extraordinarily sensitive (tension super-power), mistaking some other set-up parameter (such as string relief), or perhaps something isn't as much the same as it appears to be.
Whenever I a stuck with something that is supposed to be impossible or unlikely, I go back to what I am actually measuring and what that really means.
wait that doesn't make any cents, disregard that last one
