I have never captured any of the Enterprise digital episodes so I haven't noticed the color problems.
But could it just be the BT709 issue? US HDTV is supposed to use BT709 color for HDTV but it's unclear whether that or BT601 is supposed to be used for upconverts.
You might try my conversion filter (Avisynth 2.5, YV12) at:
www.trbarry.com/BT709ToBT601.zip
There is just a subtle difference between the two color scemes. See a side by side pic at:
www.trbarry.com/BT709ToBT601.2.jpg
- Tom