Is it possible that the source on that channel was actually 480p, and you have forced it to upscale and output 720p? I would expect native mode passthrough to pass on exactly what it detects, or is the D* passthrough capable of downrezing 720p input to 480i/p, despite 720p having been defined on your setup as a compatible output? If so, having to disable 480i/p it seems to contradict the purpose of using native mode.
I'm currently considering a switch from cable to either D* or E*, and consistent native mode passthrough is an important consideration for me. Are there issues with the implementation of native mode passthrough on D*?