I'm not sure it's so much a program problen as much as a problem with the y-harness... try plugging just one servo directly into channel 1, and that should work... if it doesn't, then the 9x has some freakie programming I'm not aware of and I can't help you much... but it should work. If so, get out your multimeter and check the continuity of the 3 cables from the male to the 2 females in question, as it might just be a break in one of the connectors that can be solved with a little soldering. If you don't have a multimeter, put the harness on channel 3 and plug your ESC into one of the females... if the receiver turns on but there is no throttle control, then it,s the PPM cable. If the receiver doesn't even turn on, then it's one of the other 2... in this case, disconnct the red power connector fron the ESC male and connect an external battery to the receiver. If you have throttle control again, then the fault is the red cable, and if it still doesn't work, then it's the black (or brown in the case of the yellow-red-brown leads) negative that's giving the problem.
Another thing to point out in case you have no experience with y-harnesess, you say about opposite direction and all that... if you are using it directly on the plane, then the ailerons will move in opposite directions. But if you are testing it all on a bench with a couple of loose servos, the servos should move in the SAME direction. What changes the direction is that the servos when ibstalled are done so in opposite directions, giving the illusion that one reverses, but really they both turn in the same direction. All a y-lead does is join all the PPM's togeather, all the positives togeather and all the negatives togeather with no electronic components involved... you may already know all this, but on the offchance you don't, just thought you should know as to know what to expect when you get it working.
Good luck!