Determining Duty Cycle on Pulse Inputs - What algorithm or circuitry is used?

Hi,

On an SDC2130, I am attempting to use the Duty Cycle of Pln3 (Pulse Input 3) as the Motor Command (Desired Motor Position) for Closed Loop Position Tracking mode. The closed loop controls work great, but I'm having a difficulty with jitters on the Motor Command (Desired Motor Position) due to the way Pln3 is reading Duty Cycle from the PWM. This issue has brought some very expensive engine testing to a halt - would very much appreciate a reply.

Setup
===============
- A Bosch automotive ECU outputs a 0-12V (nominal) 266Hz PWM on two pins
- I have these wired to the Pln3 and its ground on the DB15 connector going into Roboteq
- Pln3 is configured to use Duty Cycle as Motor Command for Motor 1
- Motor 1 is in Closed Loop Position tracking mode - a sensor is correctly hooked up

Problem
===================
- When I ignore Pln3 (No Action) and use the Slider Bar to control the Motor Command (Desired Motor position) the control works great
- However, when I turn on Pln3 as the Motor Command for Motor 1 and command a constant 50% duty cycle out of the Bosch ECU, the Motor Command (Desired Position), which is nominally 0, jumps every few seconds to -1000cnts or +1000cnts for a short time, then goes back to 0cnts

Description of the Bosch ECU PWM Signal
==========================================
- 0-12 V nominal
- But there is about +-3V high frequency noise around the 0V and 12V levels, so 0V is a cloud between -3V and +3V and 12V is a cloud between 9V and 15V
- Furthermore, the 12V high level is sometimes centered around 13-14V if the battery is well charged
- And the 0V level may momentarily rise up a bit when the ground is sinking lots of current

Questions
====================
How does Pln3 read Duty Cycle?
Could this explain my jittering Motor Command (Desired Position)?
What can be done about it?

Thanks
mike