My 3 year old has been ridden on and off for the past year, never refused a thing, or been naughty etc. She has had bumps since last fall under her jaw which my vet and I thought were eruptions. Recently (past 2 weeks) when I asked for a lope she dropped her head and shook it, holding her right ear back.  I got off right away since something was obviously wrong. About a half hour after I put her away she was shaking her head and holding her ear back. I gave her bute (this was a sunday) until I could do something about it Monday. I had a massage therapist come out and she wouldnt let her anywhere near her poll (which we thought was out) except with an Infared pad. We decided that a chiropractor would be best. She came out the following day, she was out in her poll for sure and one spot in her withers. All seemed fine right after being adjusted.
I let her sit for a few days and saddled up and it happened again. I swiched saddles, pads, bridles, etc. same result. Felt all over, pinched her spine, she never flinched until I was sitting on her back, even bareback. 
I scheduled a vet appointment, He ruled out any lameness, neurologically or physically. But OMG, we had to drug her 3 times to look at her mouth. She had 2 caps (on the eruptions I stated about earlier). Her neck muscles behind her ears were enormous, I'm assuming from compensating from pain. We ultrasounded them and all is well.

My question is this:

Could this have caused nerve damage? I gave her a week off and rode the other day, she seemed to flinch a little but I pushed her through it and she never refused a thing (she is very willing) but I could tell something was irratating her but apparnetly not  to the point of ditching me. I would hate for her to start resenting things but I dont know what else to do??

Help!