I have read all 8 pages of responses and realized that some people think that if you sew/quilt you are thankful for projects that you don't have to provide material for. Little do they know how many UFO's we have. When I was young I made bridesmaid dresses for several different weddings. When the topic of price was mentioned I usually charged about $25 per dress (this was nearly 30 years ago). It was interesting that some people thought it was a great deal and others couldn't believe it cost so much.
I think that this lady either doesn't like how it turned out or falls into the group that she thinks you should be thankful to have a project that she provided some of the fabric for.
I would proceed as you are with the e-mail and call her and talk with her directly. Ask her specifically why she isn't willing to pay the amount you both agreed to. I would not return it to her until she paid the $125 agreed upon amount. I'd also give her an itemized bill that shows all discounts.
Good luck with this and keep us posted as to how things turn out.
By the way, I think the quilt is stunning and you did an AWESOME job on it.