Some things I've noticed when running mixed (brand/type) gear:
If you're running Win98, Every time you un-plug/re-plug your USB items, a new install of it is recorded in the registry. (And like all things Mindgrosoft; it doesn't remove the old entry!!)
Are all components USB ? If so, The MS stick tends to hog more usb rescources than CH. And the twist rudder on the stick can still affect the response of it's X and Y axis even when not selected in the AH DirectX JS map.
In the calibration window, Move the stick full left while applying full right rudder. Hold the stick full left as you release the rudder, and observe the scaling window as the rudder snaps bak to center, repeat this move, but slowly bak off the rudder to center.
Any 'jaggies' in the tracking lines will show up as bounce in flight.
In the JS selection window, Be sure that the MS stick is only enabled for X and Y axis. (Just to be sure!)
Another thing I've learned; Using almost 0 deadband, and NO damping helped, But the major difference came when I set ALL the scaling curves to be identical! Especially the X and Y axis!
To see why; Move the joystick SLOWLY from center to full left, right, up, or down, and watch the line movement... Nice and smooth, huh?
Now; Push the stick SLOWLY toward each CORNER (45', 135', 225', 315'), while watching the lines, only try to keep it smooth.
Not so easy. Now make X-Y scales the same and try again, you should see a marked improvement.
Next; Jump down, turn around, pick a bail o cotton. Get all Gameport controllers, (CH, or Thrusty w/ Stickworks mod), instead of USB, and hopefully you'll be as happy as I am.
Good luck mate
S!