I spoke too soon. This problem has resurfaced now for the 3rd time. I am surprised that only a few people on the forums are having this issue.
Anyway, the support ninjas made a bug report, and they mentioned that it doesn't get much attention unless there is a group of people who are having this problem. If you are, please contact support and reference this bug report:
To reiterate the problem: Certain actions with due dates will not automatically update themselves as "due soon" with the appropriate badges and growl notification inside of 2 days out from their due date. (my pref setting) They will change, however, if there is an outside influence, such as restarting the program, checking an action in the same context or project, or changing the pref from 2 days to 3 and back to 2 again. Needless to say, it is disconcerting when OF is showing no actions due, restarting the program, and then actions suddenly reveal themselves as due tomorrow or even today.
Rebuilding the database does not fix the problem. I would like to hear if anyone else has experienced this, and please contact support if you have!