I too have seen what I'd call plough lines on some carpets (Belgium Wilton springs to mind), but they do groom out with a bit of effort. Make sure brushes are suitable (Gold/White are pretty kind on pile). I've never used HWE after mechanical brushing, only after manual brushing, so I expect that Joe's comment on wanding is very appropriate for removing lines put in during pre-spray agitation.
Pete (JS2)