A couple of ideas. One, your legs may be causing just enough heat
and abrasion to cause discomfort. If you need to urge her with legs, try
using another aid. (I like long, split reins - - I don't need to make
contact, just the "threat" reminds my mare that we are supposed to go as
fast or faster AWAY from the trailer, thank you!)
Have someone video your riding style from all directions -- if your legs
are swinging, nagging, gripping, etc., you'll be able to see it. Best to
get someone to video you who doesn't know a darned thing about riding --
less embarrassing!!
Another -- Your girth may be just a little too tight and she is getting
sore -- not enough to cause actual sores, but just enough to hurt those
muscles along her sides.
You may be riding her at a bigger trot on your rides and for longer
distances than she's used to doing. Those muscles along her side may have
gotten strained and sore.
Any of these situations may not cause raw spots, but the horse will
flinch, the skin will wrinkle and as they heal, you'll see "scurf" when you
groom her.
Where are the sore areas? At the point where all the padding stops
(and leaves a bit of a "ridge"? Is she a "rib sprung" sort of horse? You
may have to do some careful arranging to have the smoothest possible line of
padding.
I used to be a "dyed in the wool" believer in the natural fibers (wool, of
course) until I discovered "Syn Felt". I have NO idea how the stuff can
wick away gallons of moisture and still be dry by the next morning. I've
now used them as first layer of padding for at least 500 miles (of
competition) with two different distance horses and for everyday work with
all of my saddles. No matter what other padding I use, the Syn Felt liner is
first on the horse. The 1/2 inch thickness washes wonderfully in the
washing machine. I, too, use no soap.
Good luck!!!!