Some thoughts:
1. I generally use the Atkinson 1728 targets and sometimes build profiles via Eye One Match, which uses the same color engine as ProfileMaker (I wrote the article you listed above in your second post) and I've never seen a gamut plot that looks so choppy. Even when I did some test targets using the 918-patch chart, I didn't see anything like that.
2. Have you run your Eye-One through the Eye One diagnostics tool?
3. Have you tried measuring a chart by hand?