well if im right in thinking you feel this as a physical sensation, ie. its not just in your mind, have you tried focusing on this feeling and all its attributes one at a time in turn.
when i was first experimenting with meditation, for months i would get a heavy pulse feeling in my belly, sometimes it would un-nerve me, but most of the time it was just a downright distraction to letting my mind go.
then someone on another forum i used to frequent told me, the next few times it does it, just focus on that feeling with your mind, picture it, sense where it is coming from and so on, so i did and within a week the feeling went away
strange i know, and im still unsure how it worked but it did