I know how you feel. I'll give you a couple of personal examples and how I was advised by my teaching monks and got past these kind of experiences. (I also practice Vipassana)
Once I was on retreat in Lumbini, and as the retreat went on, my heartbeat kept getting louder and louder. Soon, it was so bad I couldn't focus on my breath or body at all, just this constant annoying heartbeat! It was unbearable! I just wanted to meditate in peace with my pleasant breath. I wished this heartbeat sensation would just stop. I started feeling anxious about it, and started making theories about how to solve my external problems. It must be the coffee I thought.
I went to report to my teaching monk all of this. He smiled, and said "Oh, don't feel bad about your heart! It does such good regular work for you, keeping you alive. Invite this heartbeat in for tea and biscuits, be friends with it. Observe the heartbeat just like the breath. Know when it changes, observe what conditions this awareness of the heart to arise, and to pass."
On another retreat, at the TMC in San Jose, we had a beautiful and silent meditation hall. A few days into my personal retreat, the monk told us they needed to remodel, and meditation would be held in a different smaller room, just some small space for a few cushions, table, and a clock on the wall. Well, soon enough that clock began to seem really loud. I would begin fantasizing about taking it down, or dream of talking to the staff about it "how could you place such a loud clock in a meditation room!" I'd want to say. My heartbeat and breath began syncing and getting in rhythm with the clock. It began to be a struggle, and I felt I had to constantly control my breath and heart.
In the next reporting session with the monk, I brought up the evil clock. The monk said "The clock is not problem. The problem is inside the mind."
In both these circumstances, there was a sensation that was felt to be negative. There was a resistance to them, thinking of this thing as something to get rid of, to control or change. I over focused on them, getting worked up and anxious over them, which spiraled to become worse everyday. That is, until I began to invite them in. I allowed myself to experience them completely, without trying to change them. I practiced Equanimity - it doesn't come immediately, but when you feel disliking, be aware that you are, and soften it, accepting. Know when the disliking arises, and observe it just like anything else.
Soon, when the clock or the heartbeat are no longer identified as an enemy, you begin to find pleasant feelings there too. You begin to have less and less aversion. Soon, the heartbeat or clock are just momentary friends stopping by for a quick chat, and then one goes back to the primary object, feeling even more peace and Equanimity. You'll find you have progressed, and new experiences trouble you less and less. Its all a series of friends stopping by. Just be mindful enough to know when they are coming through your door.
