The RPIs of those teams you beat during conference were just brutal, they really hurt you. You had 8 games against teams with RPIs >300, although this is out of your realm of control. Your did a good job scheduling non-conf games against decent teams to balance out your SOS, but the bottom line was you had to win more of those games.
You probably know this already, but the projection report is way more useful than RPI in projecting if your team will make the postseason.