Sounds like you have throttle blade in the wrong slot on the TPS. See if this helps:
1. Disconnect the electrical connector on the secondary stepper motor (located in front of #1 throttle body).
2. Manually open secondary butterfly and remove secondary TPS.
3. Manually open and close secondary butterflies and check full travel with corresponding TPS drive blade (located in hole where TPS slides into and looks like tip of flat tip screwdriver) movement.
4. Visually inspect inside TPS where blade inserts. Should look like a "+".
5. If all checks OK, turn on battery and bring up the diagnostic page on Tune ECU and check secondary voltage (should read .4-.6V, I believe). TPS should be spring loaded to low voltage side of scale.
6. Insert screwdriver blade into the slot in the TPS and lightly rotate screwdriver, voltage should increase until the TPS hits high side movement limit (Tune ECU readings are slow to register so take your time on rotating and reading).
7. If all checks OK, open secondary throttle half way between open and closed and insert TPS as depicted in maintenance manual. You might have to rotate it a little left or right so the blade will align with the TPS slot.
8. Without installing the screw, check full rotation of secondary throttle by manually opening and closing the bodies. On the initial opening or closing, the TPS may rotate as it is not yet adjusted. You need to be able to adjust the TPS where it is not forced to rotate when the throttle body is full open and full closed. If you can't get full travel, remove TPS and insert blade into the slot which allows full travel. Also check to insure adjustment slot in TPS is over the security screw hole.
9. Once you can open/close throttle body without TPS movement, insert screw, get out of Tune ECU, reconnect electrical lead into driver motor, open tune ECU, and follow maintenance manual for adjusting TPS (keeping in mind of above write up).
NOTE: The throttle blade can be installed in wrong the slot, causing the TPS to be off 90 degrees to the high side, 90 degrees to the low side, or JUST RIGHT. The key to this is to make sure you get full throttle body movement within the TPS travel limit.
NOTE: The stepper motor should hum when power applied and can be detected by touching the motor (it also hums for 15-20 seconds after battery is turned off). If it is loudly buzzing, then the motor is probably trying to drive the bodies and something is preventing it from moving (such as TPS being at limits and preventing throttle bodies from moving to full travel)!