KMA reflux of???

Hi everyone,
My daughter is 10 weeks old. Until about 8 weeks, she was an incredibly happy and content little girl. She still is, but I noticed something wasn't right. She arches her back a lot, and I often hear her swallowing. I went to the pediatrician, and they admitted her overnight and started her on Nutramigen (cow's milk allergy). I had initially given her Nutrilon AR, and we started that on Friday, but she didn't get better. More crying, more restlessness, lots of spitting up, not wanting to sleep during the day. In the evenings, she was so exhausted that she didn't want her last bottle. By Monday, it was so bad that I thought, "I have to stop this formula," so I slowly switched back to Nutrilon AR. She improved again, and she was smiling again! However, I do notice that something is still bothering her; she still arches her back quite often after feeding, and I hear her swallowing a lot. She also chokes around 3 hours after feeding. I suspected silent reflux even before starting Nutramigen. But if it were a cow's milk allergy, shouldn't she have improved, not gotten worse? And with Nutrilon AR, she's getting better again; if it were a cow's milk allergy, wouldn't she react more to that? Something still doesn't feel right, and I'd love to hear your opinions. It's really hard for me.