I don't know if anyone is paying attention to this topic, but I did figure out how to solve this problem... When you choose "Properties" in the 3d Mouse Home, it chooses the last program you were in. So if you have KSP windowed or alt-tab out of it and click properties on that window, you'll get the profile for KSP. That part, I already knew. However, in the current version of the software, using the SpaceNavigator (not sure if the problem is the driver version or that I'm not using the SpaceMouse Pro), it doesn't give you the option to swap axes. But if you save your profile for KSP (personally, I need the sensitivity turned way down), then it will create a config file that you can then edit. And when you edit the config file, you can swap the axes. This file should be located at: C:\Users\<username>\AppData\Roaming\3Dconnexion\3DxWare\Cfg\KSP.xml on Windows 7. This xml file consists of a bunch of Axis definitions. You just have to look for the one that says <ActionID>HIDMultiAxis_Ry</ActionID> under the <Input> tag, and change the corresponding <Output> tag to say <ActionID>HIDMultiAxis_Rz</ActionID>. Then find the one that says <ActionID>HIDMultiAxis_Rz</ActionID> under the <Input> tag, and change the corresponding <Output> tag to say <ActionID>HIDMultiAxis_Ry</ActionID>. Not too difficult. And it even seems to update in real-time, if you edit the xml file while you're playing.