Megan,
I'm not sure I had the exact same problem as you, though at one time drinking coffee was making my acid reflux (which caused me significant nausea) much worse, according to my doctor. I was prescribed a drug called Protonix, or what they call a "protein pump inhibitor." It counteracted the problems I was having in my stomach, and after taking it on/off for a year I never had the problem again.
I also wonder if you're varying your caffeine intake too much -- in other words, do you drink roughly the same amount every day? At one point before I knew about the effects of caffeine withdrawal (which includes nausea), I drank different amounts of coffee on weekdays and weekends, and I would end up feeling awful because of it. I had never realized how sensitive I was to the amount of caffeine my body was looking for. Ingesting the same amount every day solved these issues.
Hope this helps a little...good luck.
Chris