Well I actually use a hub for that very reason and for months it has kept the proper order... and now it isn't. I have an old GT wheel and a teensy 2.0 that's handling all my arcade buttons, speedo, yoke axis and ect.
The only thing I can think of is the teensy shows up as a composite device, but it's never been an issue before. I recently reprogrammed it to allow for the offsets used in the star wars yoke (the pot doesn't turn the whole way).
Anyway, I can't (easily) work on it now. I had it in the living room and the tree is now up, so I'm out of space.
The device chain doesn't seem to effect the joystick order.... I suppose some registry fudging might help, so I'll look into that later.