It is because 5000's sensor(over hanged, not press down on media like 7000), it doesn't read correctly when media buckled under the sensor, especially thicker or rigid media.
To be fair, tested 2 types of printed SAV on 5000, thick and thin, contour cut both twice on same sheet, the thick one comes out with error about 2-3mm, different cut lines, on the other hand, the thin one comes with about 0.5mm, same cut lines.
Software: Illustrator CS2, Cutting Master v1.3.