Thats actually not that bad, the fact that you lost by 7 shouldnt put you behind a team whose only loss was by a 28 point margin (especially if you are the one who handed them that loss) but if the #9 team is 10-1 its understandable that you would move behind them while they move up, its not like Boise would be forced to move back because the team they loss to earlier in the year lost, (they shouldn't be punished b/c of your loss).
Now if you finish your season with only 1 loss and you are still behind Boise then it will be a travesty. Even the BCS doesnt screw up like that, they mainly just fudge up the BCS game match-ups (like the first replier who saw a 3rd place Iowa team play for the title, now the BCS doesnt mess up that much, but they routinely only get the locked bids right (ACC v. Big East/At-Large, and the Rose Bowl Big 10 (12?) v. Pac 10 (12))
They seemed to have mastered some BCS tendencies, like how a team in the high teens (say 16) and the top 10 (say 4) and the 4 team winds up 10 while the 16 team winds up 11 despite beating the team ahead of them that past weekend.
For a long while they had the Notre Dame favoritism perfected where they had to lose 3 times to fall out of the top 25 at the beginning of the season (back in '03 they would be 2-3 and still #24)