It sounds as though this might remain an unsolved mystery then, but we can still conjecture.
If the 14/2 at the lower switch box is hot and neutral in, then the 14/3 going out must carry the neutral and two travelers. There would have to be another junction box somewhere if this is the case.
Could it be that the 14/2 at the lower switch is not actually hot and neutral but a
switch loop? (I don't suppose you can remember the connections, can you?)
I can see a scenario where power enters one light fixture box on a 14/2, there is a 14/2 run between the lights, and the other 14/2 at the second light is the switch loop down to the lower switch. The 14/3 then runs directrly between the two switches.
With this physical arrangement of cables the lights could only end up being in series. Replacing the 14/2 between the lights with a 14/3 would allow proper operation.
But as you said, you'll probably never know.