Another "this topic is very old" post but I think its better to keep this information contained in one post because I feel that not many people are affected by this issue or typically use 3D mice for KSP (but they should it mimics real life translation controls in spacecraft for RCS controls for docking). This issue is still present in the most recent update.
Also, I find that the settings for 6DOF controllers are rather lacking. One request I have for the devs to look into is allowing us to configure the axis for controls. For example switching which axis controls rotation/translation. As well as disabling certain axis all together. My preferred use case is to disable the pitch and yaw (possibly roll too) and only use translation controls for RCS manuvers. However, I would still like to use the full 6DOF when using camera mode. The only workaround I have currently is to disable p/y/r in the 3Dconnecxion settings for "KSP_64.exe" completely, which does not allow me to use those rotational controls for camera mode.
Again sorry for somewhat necro hope you understand given the circumstances.