As I've said, I have a mate who is heavily into Sahaja yoga (the kundalini thing). He also happens to be a medical practitioner (works in the hospital system). His take on it is that he has acquired an ability (a kind of discipline) by which he can switch on "feel good" parts of the brain. In this way he can avoid "negative" or counterproductive thought patterns and just "be happy".
My mate tells me that Buddhist monks who meditate a great deal have subjected themselves to brain scans which show that the "feel good" areas are almost constantly "lit up" where most of us spend significant time in the "feel bad" area.
If this is true, a disbelief in chakras/qi etc. (which I have - I too am a barabarian in this sense) would not necessitate disbelief that meditation might confer benefits of a potentially significant kind. After all, an ability to have such a high level of mental discipline that one can control what are usually thought to be autonomic processes seems very useful if not life-altering (think of dealing with chronic pain, depression, grief, loneliness etc.).
However, the question remains - is any of this really true? I can only go by second hand accounts and I have not personally seen/read any studies into brain scans etc.