Not that it is an official solution for these issues, but has anyone considered or tried using
PhoneAlarm?
It integrates with the notification system and in fact, basically takes over. I've had some better luck with "waking up" for alerts, reminders, emails, and SMS with it. Heck, it doesn't seem as if if PA could actually make this any worse either...
Maybe someone here should give it a shot and report if it at least ameliorates these problems. (yeah it stinks to have to do that, but as a workaround it might be worth it).