Not to worry, I dug this up:
Approved unanimously by the Owners' Committee during the Winter Meetings of 2011-12.
MLB, Rule 74, Section 3(a):
In the calculation of the final winning percentage of any team during the regular season, the first three (3) games shall count 'less' than the final three (3) games of the season. Upon the completion of Game #162 of any team's schedule, Games #1, #2, #3 will be stricken from calculating the final winning percentage and a team's final record will be calculated based on a 159 game total, beginning with Game #4 of the season. The application of this rule will supersede all playoff seedings based o the 162 game schedule.
So, all is good. These 3 losses will be stricken from the record on October 1.
I always wondered why they didn't put this rule into effect last year; we would have made the playoffs....