(I have no idea if CFS is "in your head" or not. But even if it is, it can still be totally real.)
Sure. In-your-head diseases exist, and they're very real. Placebo effects, for instance, have been very conclusively shown to be extremely powerful - there's no question about the reality (though some still do...). But the odd recurrence of Epstein-Barr is very odd if it's all in your head.
1. The effects of the disease aren't in your head at all, they are very real, and
2. The cause happens to be in the brain rather than some other organ of the body, but it is not available to the conscious, thinking mind.
That doesn't mean that we should stop researching non-psychogenic causes for common ailments, as has been mentioned, ulcers and even some forms of CFS have been shown to have a clear cause and treatment. However, it seems a shame that this entire line of research has pretty much been abandoned...what happened, after all, to the hysterical diseases that Freud was successfully addressing in the early part of the last century? I doubt very much that they just stopped occurring.
Thanks.
BTW I couldn't see an email address in your profile.