If you mean why Menard wasn't locked in due to the top 35, that is because the #15 owners points went to the #1 of Truex, while the #1 owners points went to the #15. The #1 only ran a partial schedule in 2005, so therefore the #15 which is using the #1's owners points from the year before was not longer locked in for 2006.
A similar thing happened in 2009 with SHR. Scott Riggs put the #66 team into the top 35, while the team car, number #70 was not. Therefore Stewart gave the #66's owners points to Newman, since Tony could rely on his past champions provisional to make the show, being the most recent champion not locked in(since he was the 2005 champ)