I agree that this is a strange symptom, and it is a little hard to know what to make of it. I would recommend discussing this issue again with your regular primary care doctor
Suboxone can occasionally cause nausea as a side effect, and I do wonder if this might be what is going on. I'm thinking here that you likely are taking the suboxone when you get up in the morning, and that shortly after this you are applying your eye makeup. If this is the case, then the nausea might be just from the suboxone, but you might be making a false association with applying eye makeup, since the two things are occurring in close succession.
Another possibility, which seems less likely, is that you might be triggering an usual reflex known as the oculocardiac reflex. This is usually triggered by pressure applied directly to the eye ball, and I wonder if you might be inadvertently triggering the reflex, which leads to slowly of the heart rate, which might be quite unpleasant (although usually quite transient) and make you feel nausea.
I would recommend discussing this issue again with your regular primary care doctor, especially if it continues. They can consider these suggestions and also perform a physical exam to make sure there is nothing more serious going on.