Looking into it further, looks like it was just a "tough call" for the engine. If you look, SOS appears to be the difference-maker and not overall RPI and not ranking at all.
The #1 seeds:
Wilmington: 26-4 Rank: #4 RPI: 4, SOS: 16, 21 straight wins.
Fayetteville St.
27-2, Rank #10, RPI 5, SOS 25. 10 straight wins.
Wisconsin Parkside
26-3, Rank #7, RPI 1, SOS 9. 10 straight.
St. Edwards.
28-1, Rank #9, RPI 2, SOS 34. 17 straight.
Two #2 seeds of note:
W. Washington
29-0, Rank #1, RPI 6, SOS 71. 29 straight.
Mercy (oldresorter)
27-2, Rank #2, RPI 8, SOS 35. 27 straight.
I made W. Washington's schedule as tough as I thought I could, just a few perennial powers were on bad years, hence the bad SOS. I withdraw my complaint.