I had a brain and upper spine MRI w/contrast last year to rule out MS. I had 2 areas of "increased T2 Flair signal", which the neurologist said they were nothing to be worried about, and that they could be explained by me being a migraine sufferer. While this is very possible and my MRI results definitely showed nothing alarming, my ME/CFS specialist thinks it is a good idea to do a repeat scan at some point just to be cautious given I have a lot of neurological symptoms, some not explained by ME/CFS. Seems like a sensible plan to me.
As for ME/CFS possibly being caused by the brain, I am very doubtful this is the case based on the research coming out. In studies showing brain abnormalities in ppl with ME/CFS these abnormalities do not always persist. In that a person can have a test showing abnormalities one day and then another day the same test is normal. This is an encouraging finding as it points any brain changes likely being reversible, and not permanent. Just my 2 cents.