Oh, there are so many things that could cause this.
1) Do you have a lot of supply right now? Does your baby also cough while nursing? It could be that you have an over-supply issue or forceful letdown, which can cause these symptoms. (http://kellymom.com/bf/supply/fast-letdown.html)
2) Reflux can be aggrevated by food sensitivity. For my son, it was dairy - I cut out all milk, ice cream, cheese, even products that listed milk as an ingredient and he was much happier.
3) A rule of thumb for nursing a reflux baby is half as much, twice as often. Definitely keep her upright after eating. Also check out kellymom.com for reflux tips (http://kellymom.com/babyconcerns/reflux.html).
Also, if I can give you a tip - a moby wrap is the best friend for a mom of a reflux baby, because it holds your baby vertically against your chest. My baby spent many hours napping in the moby wrap because that is how he was most comfortable (and I needed to get things done sometimes).
I breastfed 2 babies, one with severe reflux and dairy sensitivity and I had an oversupply/overactive letdown issue that aggravated it. And as you can tell, kellymom.com is my go-to website! Please feel free to PM if you have any questions about any or all of the above issues. I've been there. And I could post a lot more tips that worked for me, but I don't want to overwhelm you with things that might not apply to you right now.
Good luck