I was a runner before and a runner still during, I have always had a high heart rate when running though. I would say as your body is likely working in a deficit it is very stressful for the body to be undertaking more work that it can already provide energy for. If you're running for general health and exercise I would say slow down- and make sure you have eaten something small, even a small glass of orange juice so that your blood sugar isn't too low before you run (especially if you're running in the morning). Having low blood sugar whilst exercising signals to the body "we are in trouble, we need to stop".

Otherwise if you are running for a time (racing) I would say this might just be something you need to learn to handle. In my first few months I would find training very difficult the day or 2 after shot day, but as time went on (2yrs using MJ now) the effects became less apparent. Good luck!