Somewhat. If a shot had a lot of motion at the head and then not a lot of motion at the tail I think CCE was thinking there was a scene change and the compression would go from good to no-so-good in the middle of a shot. For example, if there was a swish pan to static shot with some people sitting around the compression would hold up in the pan but then the people would get a high compression. To get around this we ended up checking everything in the advanced options which seems to have given us a full-on CBR without any matrices, which is fine for us because our content was short enought to not have to worry about a high bit rate.
As for the work flow, we ended up going with the downscale from HD to SD from After Effects. We had to go through the show and add blur (Fast Blur) to a handful of shots to keep them from wiggling, mainly high contrast shots with thin horizontal lines and subtle movement, but the result is pretty good. Compared to a Blue Planet DVD our AE downscale was much sharper, but if it were up to me, I would have went with a downscale using the deck (AJHD1400). It would have looked softer, but it would have been more consistant, like the Blue Planet DVD.