It seems that the iqm tool repositions all meshes whose pivots aren't zeroed out to the origin at x;y;z 0;0;0. And bones that are not attached to the root bone breaks the animation, i.e if you have 2 roots (like in the example).
https://www.dropbox.com/s/pffl9t2ssk58sw8/animTest.zip?dl=0
It seems that the iqm tool repositions all meshes whose pivots aren't zeroed out to the origin at x;y;z 0;0;0. And bones that are not attached to the root bone breaks the animation, i.e if you have 2 roots (like in the example). https://www.dropbox.com/s/pffl9t2ssk58sw8/animTest.zip?dl=0