Since her father has MS, I suspect that he has an X chromosome with duplication of at least some of the short arm of the X chromosome. She inherited this defective X and can not establish effective epigenetic control over the genes from that region.
This might be similar to X-linked chronic granulomatous disease (X-CGD) where there is a disruption at Xp21.2. X-CGD has a defective gene needed for generating oxygen radicals in macrophages that digest bacteria with an 'oxygen burst', sort of burn up the bacteria. Without an effective gene, the bacteria persist and these boys usually die young from bacterial infections. X-CGD affects males but not females since females inherit a good X chromosome. However, there are reports of lupus-like symptoms in some boys with X-CGD who have a duplication of the X chromosome from Xp21.2 to the teleomere. Also, some mothers with X-CGD sons also show lupus-like symptoms. I believe these mothers may have had duplication of that section of the X chromosome also, rather than just a single point mutation at Xp21.2.
We have discussed X-CGD previously and I hypothesized about two polyamine genes at Xp22.1 that, if over-expressed, would cause an excessive and wasteful demand on the cell's S-adenosylmethionine supply and hamper the cell's ability to methylate DNA and proteins.
I am currently writing an updated version of this X-linked polyamine enzymes hypothesis which I expect to get published soon. Then I can go into more detail. For now I am trying to organize my thoughts on it and get it down on paper with the references. We discussed it about five years ago but since then I have been able to tie in a lot more of the autoimmune disease features and events. I need to publish the updated ideas so it might help me get funding to do drug discovery on it. Drug discovery is my job but currently only on cancer targets for other researchers projects.
Another possibility is that the girl can not establish effective X chromosome inactivation, and therefore winds up with over-expression of some X-linked genes. This would also have similar consequences to the short arm duplication.