Have you had an equine chiropractor look at her? This could be her back, but it could be her neck or almost anywhere on her, so many of these things radiate pain to unexpected places. It can also be somewhat erratic in where and when it hurts them.
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Christie Keith
Caber Feidh Scottish Deerhounds
Holistic Husbandry since 1986
www.caberfeidh.com/