I don't know if you have solved your issue yet, but I think I may have found a solution. I was working on the same problem myself and found that the getJacobian() function returns the Jacobian in the base frame for the JointModelGroup that you specified in the request, not world as I originally expected. If you want to rotate the Jacobian to a different reference frame here is an example of how you might do it. I have not verified this code but it looks like it should work. Note that the getGlobalLinkTransform will not work if the base frame of reference of your group is not the same as the global frame, which was the issue that I ran into with my robot. If the base frame is different than the global frame, then you could use getGlobalLinkTransform to get the transforms for both the base link and the EE link, then use the two in order to compute the relative transform between base and tip. Then use this relative transform in order to rotate the Jacobian into the EE frame.