It seems to be an issue with the nested groups. If you open the newer file in Inkscape, while you can see the colors, if you click any of the objects, you'll see "Paint is undefined" in the `Fill and Stroke window.
A simple fix is to simply remove the extraneous groups.
- Open the file in Inkscape.
- Press Ctrl+A to select everything.
- Press Ctrl+Shift+G to ungroup.
- Click one of the colored objects and verify that its fill color shows up in the
Fill and Stroke (Ctrl+Shift+Shift+F). If it still says "Paint is undefined" try ungrouping 1 or 2 more times.
As you might have noticed, Scribus is a little more strict about the features used in an SVG graphic. Most SVG editors have special features in SVG files in their own namespace that Scribus doesn't understand. Inkscape can "figure it out" in this case and show the correct color, but Scribus couldn't. To debug this type of thing, I usually open the SVG in Inkscape with the XML view and walk through the image. Usually the root cause is some hinky XML in the file that can usually be removed. Saving as "Plain SVG" from Inkscape can also sometimes help (but didn't work in this case).
(Tested with Scribus 1.4.5 and Inscape 0.91)