Do her withers shake a whole bunch when you touch them? My vet does chiro and acupuncture also and I hadn't thought of my mare twitching her withers as causing pain, I just figured it was because I was touching her lightly and she was just shooing it away like a fly. My vet said if she just spazzes and twitches for a long period of time while I'm touching her, it's a lot of muscle spasms causing pain. She called it "wind", I guess that's the acupuncture term. She did some and the twitching stopped.
It's started up again and she snips at me if I brush her withers with my hand.
That might be something to bring up with the chiro too.