The horse may have back pain and connect it to the saddle.
If you check and she doesn't have any, it might be that it pinches his scapulas or withers.
It might also be a bad memory but that is a rare case.
If the saddle is checked and still fits then check for rubbing or bruising caused by a saddle pad or numnha as it may caused discomfort, if all is good and the horse is just worries try just giving them small treats as you tack them up and talk very softly and calmly
If she just shying away and this is a newer habit the saddle may not longer fit and she's associated it with discomfort.
If the's bucking to the saddle she's possibly only sensitive, look at this exemple of treatment if it could help you.