I don't have that problem, when I use drogues for my Dragon capsule. Are you moving the drag point, far enough away from the capsule ?
Now that you've asked I'm not sure. at the moment I'm using the attachment point of the drogue to the capsule which is where, in theory, it should be
I just posted a thread on the subject here
http://www.orbiter-forum.com/showthread.php?t=30996