I have tachycardia, which is what this sounds like, and for me it was very difficult to diagnose because it would only happen sporadically and sometimes not for weeks. Here's my story.
It was about 20 years ago. It was not related to running. I was having episodes where it felt like my heart was actually stopping for a few seconds (it was actually beating faster). I would have to catch my breath. Very uncomfortable and kind of scary. It would happen every couple minutes for around 5-10 minutes. Then it would go away. Sometimes it would come back another 15-20 minutes later and continue doing that for an hour or so. Then it would go away for days or even weeks.
Doctors couldn't diagnose it because it would never happen in their presence. EKG's were normal, I even wore a Holter monitor for 24 hours, but the episodes never happened during that 24 hours. The cardiologist said everything was completely normal.
The cardio prescribed a stress test, and the morning of, I noticed the palpitations had resurfaced. I went to the appointment, didn't say anything but the doc put his stethoscope on me to give it a listen. I could feel the palpitations starting. Suddenly his eyes lit up, and he told the nurse to hurry up and get the EKG hooked up. She did very quickly, and they got a BEAUTIFUL snapshot of what was going on, and as soon as the doc saw it he said, "I know exactly what this is." It was a type of tachycardia, not dangerous at all, and he said my options were to take a pill or get a surgery to ablate it.
I went for the pill (channel blocker), and have been taking it for 20 years now with no issues and only rarely a faint palpitation but it's completely controlled. I see a sports cardiologist once a year and everything is good. I'm 62 and run 25-30 mpw.
So this sounds very similar to what you are experiencing. The thing to know is--they will never be able to diagnose it unless the palpitations occur while they are observing you and can get an EKG during an episode. When the episodes aren't occurring, your EKG will be normal.
So you need to find a way to get an EKG/Holter while the palpitations are occurring. That can be tricky, but if you can do that you'll be good to go.
Good luck!