Yes, I have had saddle fit checked and it fits her very well. I am looking into getting a new saddle at the moment because even though it fits her, it's awful for me! So we're seeing if we can find something else that fits her but is a little better for my position.
The fact that you're not comfortable could be the cause of your mare's issues. Turn the equation around: the saddle fits YOU, but it's not so good for your mare. Not very fair, is it? I have tons of customers who tell me, "I don't care if it works for me, as long as it fits my horse." If the rider is uncomfortable, it's going to effect the way they ride and their balance, which in turn will effect the way the saddle fits, which will eventually make even a well-fitting saddle uncomfortable for the horse. The saddle needs to fit BOTH individuals; if only one is happy, the other will be miserable in pretty short order. And given that your mare's still somewhat green, you want to make her under-saddle experiences as positive as you can ... and that's tough if you're struggling for balance or trying to compensate for discomfort. I'd recommend getting a different saddle sooner rather than later, and perhaps focus more on longeing and other groundwork until you have a saddle that suits you both.
^^ What she said. Think of the saddle as the 'interface' between horse and rider. Its job is to balance the weight of the rider over the horse's back as best as can be. An the first part of that .. Balance the rider !
If the saddle is a 'technically correct' fit for the horse right now, beware of adding too much bulk under it - I will typically use a Mattes half-pad where the saddle is slightly wide, since it will slightly narrow the fit. This will raise the pommel slightly relative to the cantle, move the rider's seatbones back, and incidentally, tends to give the rider more flap in front of their knee - so for example, I have seen a rider who feels their leg is too long for their jump saddle and they need a more forward flap, when what they actually need is their saddle to be balanced.
You should probably try different pads before you buy ... are there other people around in the barn who would let you play with the various pads and see how they change the fit ?
Oh, forgot to add: gel pads aren't all they're cracked up to be. They're heavy, and their own weight will pull them down onto the spine. They don't alleviate pressure (think of it: you poke them, and the gel moves away. How's that cushion anything?). They also don't breathe; I had a client scald her horse's back by using a gel pad at a show on a hot day.
When I say the saddle is awful, it is perhaps a bit of an over dramatization. I certainly can't stand it, but it isn't truly horrible for my position. I just have to work a bit harder to maintain the basic balanced position and a line shoulder, hip, heel. The stirrup bars are set too forward for my leg so I'm pulled into a bit of a chair seat. However I can correct it, it just takes some effort.
Currently I am not the one riding her, I am away at school. So my friend and trainer are both working her. Of course, the saddle fits them just fine! They've both been blessed with much longer legs than I. So I don't think her discomfort is related to poor saddle fit on my part.
Thinline sells their seconds on Ebay for about $45. Sometimes the edges are a bit crooked or the print is blurry but the material is the same.
I've bought a few of these in the past and all have been in excellent shape with just a slightly blurred logo like enjoytheride mentioned. They put a few more of these on ebay a few days ago (they put a handful of them up every few months-ish), but they may all be gone by now, they tend to sell pretty quickly (they list them as buy-it-now, not auctions).