I found out what the problem was I believe. All calendars, everything were set exact. My project calendar was a "Calendar days" with 7 days a week set. The problem was when project 2000 calculates the lag/lead time, it uses the project calendar, or in my case, the calendar days which means a 5 day lag was 5 calendar days. In project 2003, the lag/lead time will only use the project calendar unless the successor has it's own calendar (which it does-5 day a week calendar with holidays added) so it uses that calendar to calculate lead/lag duration, so a 5 "calendar day" lag in project 2000 becomes a 5 "working day with holidays" lag in project 2003.