"Epigenetics" is just one way of saying that an external factor has more impact than the DNA itself does. Hence a standard genetic test wouldn't show epigenetic changes.
Maybe I misunderstand you here.
As I understood epigenetics is, amongst others (mutations would be the other), something like a "switch".
The genome is like a big database with lots of "recipes". The cell reads parts of genes in order to produce proteins/amino acids. Epigenetics would be an external factor influencing which part(s) of the genome are read out (by a cell) or not. So, epigenetics is, amongst others, about which external factor will lead to which gene expression and in which amount.
"Epigenetic aberrations are also important for the development of immunological and neuronal diseases..."
http://epigenetics.uni-saarland.de/de/home/
I am certain there are aspects we don't know yet.
I don't know when the first cases of ME did appear - is it 200 years ago, 100 years...? Our environment changes constantly, and I'd expect changes in livings' DNA due to that - new illnesses, new skills, new looks and more.
The problem with novel mutations (not inherited) is that they can't really proliferate enough after childhood to cause problems, unless the mutation results in uncontrolled growth, in which case we'd be diagnosed with cancer instead.
Mastocytosis is a counter example, although I agree that in general mutations would lead to a (swift) destruction of the organism (death).
Heteroplasmic mitochondrial mutations are a possibility, and I don't think there have been good studies involving muscle biopsy in ME patients yet, which is what is generally needed to detect such mutations. Though it sounds like the NIH on-campus study might be adding that.
This is very interesting!
I had thought in that direction and think about getting active. At first I decided against it because an ME expert told me most patients report no findings. But I am not sure how thoroughly it was looked (many patients are categorized as "psycho" which leads to no or bad diagnostic, so...).