Have you ruled out sleep apnea as a cause?
Not to offer a diagnosis, but you might want to google something called 'noctural panic attacks.' The way these things manifest themselves is apparently *extremely* different from what we normally think of as panic attacks, but palpitations are part of the picture. Here are a couple of links to the condition:
http://web4health.info/en/answers/anx-panic-night.htm
http://www.mayoclinic.com/health/panic-attacks/AN01760/
It sounds like I have identical symptoms that you have waking up at night with rapid/irregular heart beats and they are severe. This has been on going for about 15 years; I'm usually dreaming and I awake and the symptoms are so severe I wake my husband and we start to head to ER but it always settles down before we get there. It is so frustrating and I have been to dr. after dr and they can't seem to pinpoint it. I was told I have sinus tach, but they say it is abnormal in that it only happens at night and never during the day. I would really like to get to the bottom of this. I have just spent 3 days in hospital doing eeg recordings to see if that would show us anything.
I WOULD LOOK INTO PERI MENOPAUSE THAT COULD BE SOMETING TO DO WITH IT HORMONES MAKE MY HEART GO CRAZY!
I have a medtronic device inplanted because they weren't able to find my source of tachycardia (they have since found it). I took some times wake up with a pounding heart. I decided to record it with my device to see what it was the next time I had my monitor read. I had a 3-5 beat run of PVC's, which the cardiologist said nothing to worry about.
Did the monitor capture one of the nocturnal events? If not, you may want to talk with your doctor about wearing an event monitor. It is worn for a longer period of time and you can "record" activity as it is happening. You are probably just fine, but I always like to know that the doctor SEES when I am describing when it comes to my heart rhythm.