i am not sure about 2009, but, 2008 5MT PZEV does not have a rev match feature. I do not think that 2009 5MT is significantly different from 2008 in this respect.Doesn't the 09 5mt have a rev match feature? Could this be a malfunction of that?
I agree, get a data trace. Compare accelerator inputs (there are two) with throttle position, might find something interesting.