Some years ago Dr Samuel Donta published on SPECT scans -'Brain SPECT scans are abnormal in most patients with chronic Lyme disease, and these scans can be used to provide objective evidence in support of the clinical diagnosis. The use of certain antibiotic regimens seems to provide improvement in both clinical status and SPECT scans.'
http://journals.lww.com/nuclearmed/Fulltext/2012/09000/SPECT_Brain_Imaging_in_Chronic_Lyme_Disease.33.aspx
It is not uncommon for patients with ME/CFS to have Lyme Disease
http://www.iacfsme.org/BULLETINWINTER2011/Winter2011ShorCFSinLyme109123/tabid/458/Default.aspx
Dr Montoya at Stanford is currently looking at immune system disruption, inflammation and pathogens involved in ME/CFS.some interesting links and information
http://stanmed.stanford.edu/2014fall/immune-system-disruption.html
Some time ago Mayo published interesting work on MS finding that it was an outside in process rather than inside out as previously thought
http://www.businesswire.com/news/home/20111207005102/en/Mayo-Clinic-Collaboration-Finds-Multiple-Sclerosis-Starts#.VFUVjTSsXPA
Maybe with further research and scans looking at Function SPECT, PET or fMRI we may get some answers and very sick patients will not be shown the door when the current tests used are 'normal'