I ran the Puma helicopter simulator project for the RAF for a while. It wasn't at all uncommon for pilots to feel uncomfortable in the box because the eyes often told the brain something that the seat of the pants knew wasn't actually happening.
The more experienced the pilot on type before he went in the sim for the first time, the more likely he was to feel ill because he knew what he should be feeling through the seat, and didn't!
One pilot had to terminate the session for the day because he "crashed" the sim from the hover (not unusual to begin with, due mainly to a lack of visual cues). He had previously suffered a wirestrike accident in a Gazelle and "rolling it into a ball" again completely threw him out of kilter for a while.