I don't believe they do. On the NYC Marathon website, the qualifying times are shown WITH seconds (e.g. 2:55:00), whereas on the BAA page that lists qualifying times for Boston, the times are listed without seconds (e.g. 3hrs 50min), and they explicitly say "An additional 59 seconds will be accepted for each age group time standard. For example, a net time of 3:50:59 will be accepted for a 42-year old woman."

http://ingnycmarathon.com/...applyfor2006_new.php

Just run 2.25 seconds per mile faster during your marathon attempt (or 4.5 seconds per mile faster for a half)! Good luck!