Going 3-7 in your non-conference schedule did not do any favors for you.

Not sure what this will say, but let's look at the numbers:

Whitworth: 17-12, RPI 63, SOS 15, 3-7 Non-conf, RPI 1-50: 0-5, RPI 51-100: 6-5, RPI 101-200: 3-2, RPI 201+: 8-0: Listed 3rd on bubbles burst
Chapman: 15-12, RPI 61, SOS 9, 3-7 Non-Conf, RPI 1-50: 1-7, RPI 51-100: 3-3, RPI 3-2, RPI 201+: 8-0- looks to be last At-large in

Pretty close.  If I was a betting man, I would say the win over Baptist Bible (#12 at the time, 29th RPI) and the two spots in RPI were the difference.

Couldn't have been any closer. In real life, with a human committee,    Whitworth's two wins over Chapman would've given them the nod. Unfortuately, in WIS, head-to-head results aren't a factor in at-large bids. 

Chapman was pretty lucky anyway. It's rare that RPI 61 gets a DIII bid