I started getting odd pains in my hands and wrists ever since moving from scissor and straight rubber dome to Cherry MX brown/blue several years ago. Not carpal tunnel — this is the pinky side of my hand (forget what that one is called). These pains are annoying, and come and go every week or two.
I still have my MX blue at home, but at work I've been back on my Realforce for a few months, for a change. My hands and wrists feel all the better for it (though as I write this, I've just started getting a bit of pain in both hands!)
It may be that, no matter how adjusted I am to MX switches, I'm still suffering from the hard landing of the switches. I don't know. Personally I prefer MX brown, but my wrists most definitely prefer Topre ;-)