Reply to Controller issues in Traktor

So here's the issue, I have an Ion Discover DJ and Numark Mixtrack. In Traktor, I'll used a tsi file that I found on the net, and when I got Mixtrack, used it's tsi from the CD it came with. Then when I replugged the Discover DJ, it remapped the buttons and stuff natively (as in, it didn't use my old tsi file, but remapped it another way).

In short: I want my Mixtrack to work with decks A & B and my Discover DJ with C & D, but modifying one changes the other.

Sorry if this was a bit confusing, but any help as to why this is happening would help a lot. I'm wondering if since they're the same maker, if the MIDI signals be similar, that they're getting confused? But I don't believe that's the case because I've seen the 2 deck midifighter video.