According to code, and your house was built after this rule was made, every switchbox MUST have a neutral for that circuit. The standard now is that the neutral MUST be white or gray. But i don’t know what the standard was in 99. That being said, just because when you put two wires together the upstairs switch works, doesn’t say anything about the wires. You could be connecting the traveler and the hot downstairs. In that case , the upstairs would also work.
Why do you keep saying “traveler 2”. You don’t have two travelers. The upstairs has a line, load, neutral and traveler. The light you are trying to switch is upstairs, isn’t it? I think your original switches were wired this way:
So you can see, the second switch there are only 3 wires. How the line from the box, the white and the red…this is because 3 conductor wire comes that way. The colors are meaningless. If this is the case, then then one of the black wires coming into that box is the “real” hot. Does that help you?