Wierd.I have a couple of ideas, but I may be way off. If you have IBS or acid reflux, and your stomach is producing too much acid, it may be backing up into your esophagus thus causing what's called a sympathetic response which can then lead to heart dysrhythmias (though I've never heard of acid reflex being directly associated with dysrhytmias) and possibly palpitations.
Or heres another compeltely off the wall, half science, half science fiction idea. Perhaps the building up of CO2 in your gi system is diffusing into your blood stream some how, and displacing oxygen and thus causing a dysrhytmia and palpitations???
Bottom line is that I don't know, but these are some fun ideas to kick around.
Zach