Let me get to the point. Understand, some information may not be 100% accurate, but it should get to the point.
The masters that Cartoon Network had recieved were SD Digibeta tapes, which have a resolution (or roughly) of 720x480i, which was commonly used in Standard Definition broadcasts. While I am not 100% sure if US broadcast use these, standards in Japan use HDCAM, which has a potential resolution of 1920x1080, or as most broadcasts are, 1440x1080, with it stretching to 16:9. What is happening here is CN is upscaling the digibetas that they had for Eureka 7, from 720x480, to 1920x1080, or potentially 1280x720 (as I believe that's what the channel broadcasts at, atleast in my area).
Because CN is upscaling footage of Eureka 7 to 720/1080, they are introducing additional problems, as the upscale isn't... perfect, with interlacing problems showing. Samurai 7 is an HD produced show, though is somewhat of a softer show (it should also be noted that each shot may not always be the same resolution). Notice it does not have the similar problems as Eureka 7 in terms of upscaling.
The problem here is there is an HD master for Eureka 7, but CN nor Bandai (despite coproducing it) have access to the material. That or Bandai does not have the budget to put together a new master for CN's broadcast, which either could be the case. Another problem with your claim is that the masters would be sent 1920x1080, Pillar-boxed, as that is how most HD masters are prepared. Even masters on Japanese TV that have an aspect ratio of 4:3, are still pillar-boxed and stretched from 1440x1080. Blu-ray, also, as far as I am aware, to spec is always displayed as 16:9, 720p/1080i/p, regardless of the resolution (as the format can do 1440, but it is stretched). Other resolutions on that are therefor stretched or not stretched, depending if the flag for 16:9 is selected.
I should also note FUNimation sent CN/AS the Yu Yu Hakusho episode with the BD master, and it was 4:3PB. It was quite obvious for those watching the Standard definition feed, as CN neglected to crop the feed.
I also have noticed some channels can properly change the aspect ratio on broadcast, but there may be a chance said broadcasts may simply be hard encoded 16:9, or 4:3PB, or just simply stretching the footage. Which, essentially, CN does with all their content (as well as Turner), unless they have a proper Pillar-boxed master.