I have certain calendar event reminders that are not issuing on the iPhone (3GS, latest iOS 4.3.5) after syncing from iCal on the desktop with a CalDAV calendar running on Mac OS X 10.6 Server.
Most appointments do issue alerts properly, but I've noticed ones that have some or all of the following attributes are a problem:
1 - recurring on alternating weeks
2 - alarm set for day before the event (e.g. 7pm the night before or "5 hours before all-day event" as calendar sees it)
3 - alarms that do not conform to the short list of pre-set iPhone calendar alarms (5 min, 10 min, 15 min,... 2 hours before, 12 hours before)
I have a feeling it's #3 or a combination of all. I've tried deleting and re-adding the calendar on the iPhone. I've also verified that the time zones match between phone and desktop iCal. In my case, the alarm never happens for these specific events, not that it happens much later or something.