under13: Has the switch always been that way? If so, it sounds like the wiring is reversed. Another possibility is the motor plugs on the Leslie amp were switched around. Check the Leslie amp. The fast motor plugs should be on the left and the slow motor plugs on the right (the fast motor plugs are brown and the slow are white). If they are in that order then it's very likely the wiring in the switch. A very simple workaround for this is to reverse the motor plugs so the slow motor plugs are on the left and fast to the right.
The wires from the switch that connect to the wires on the Leslie kit aren't polarized so it definitely sounds like to me the wiring inside the switch assembly isn't right.
As for switch preference, I like the good ol' halfmoon switches. I did play a C3 that had the TrekII switch and it was okay. I've also played a Hammond A100 that had a 6122 style switch (a small box mounted under the console rail, has 2 white knobs) and hated it. I bought a halfmoon for my Hammond CV.