This is almost like De Ja Vue.... I can certainly relate.
My mare would avoid saddling when I had her tied (I don't cross tie, only the farrier does that) and try and walk away. When I would have her smell the pad, her head would go up and back would freeze. I kept trying to get her to RELAX and did the desensitizing with the pad - I think it even got worse - she would NOT relax, but would just stand and let the pad be on her back. Ears were back, back was tight, but she would lick and chew almost like, okay, get this over with and just saddle me!
Have you tried just swinging the saddle on her back? Is there any difference? Mine will stand when I swing the saddle on her back - without the pad, both sides even. So that made me realize it may have something to do with the pad. I suggest going in a round pen and try desensitizing her to just the pad, a towel, something light. (I was practicing my Level 1 Parelli so I practiced tacking from both sides). Then try your saddle - alone - and see if there is a difference. You may have to pretend you are training a NEW horse and start from ground ZERO and work up. Sometimes they react out of the FEAR of something in their past. And not so much by what you are doing NOW, but they are afraid of what might happen next.
I had a 1" closed cell neoprene Classic Equine. I then bought an open weave (double - 2 layer) neoprene with extra foam in the wither area to bring the saddle above her withers. She does not flinch now when I put this pad on her back. I had white hair areas with the closed cell pad, and even went to whittling the pad down, cutting holes in the areas where the white hair was forming (which was the area where the stirrups are attached in the western saddle) Didn't work - she hated the pad.
