Well, a couple things... if you are hearing a rhythmic noise coming from the tranny, you might pull the CPS and check the end. It has happened before that the CPS will start interfering with your reluctor ring on your flywheel/flex plate. This is often the case if your flex plate/flywheel is cracked or warped. I have had it happen before at any rate.
I don't know on your particular motor, but if it has an inspection plate you might check it.
I think some of the newer CPS's sit in an enclosed pocket, so it wouldn't strike the CPS, but the ring could still be damaged causing a slight oscillation, which would set off an error.
Something to check anyhow.